Variant report

Variant	rs3093978
Chromosome Location	chr6:31498497-31498498
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31461526..31464326-chr6:31496464..31498692,2	K562	blood:
2	chr6:31495666..31498592-chr6:31587530..31589995,2	K562	blood:
3	chr6:31464473..31467635-chr6:31497399..31499705,3	K562	blood:
4	chr6:31494838..31496552-chr6:31497130..31499427,2	MCF-7	breast:
5	chr6:31497072..31502351-chr6:31549039..31551366,5	K562	blood:
6	chr6:31461159..31464326-chr6:31493652..31499334,8	K562	blood:
7	chr6:31496727..31498711-chr6:31590838..31593698,2	K562	blood:
8	chr6:31495999..31499455-chr6:31625533..31627883,4	K562	blood:
9	chr6:30582838..30585806-chr6:31497369..31500539,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000227507	Chromatin interaction
ENSG00000201680	Chromatin interaction
ENSG00000204511	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000200816	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000204516	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000225499	Chromatin interaction
ENSG00000227198	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1129640	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516393	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516394	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523502	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523508	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523510	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523511	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093948	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093950	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093976	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093977	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3093979	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093980	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093981	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093982	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093983	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093984	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093985	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093986	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3093990	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3093995	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094001	0.87[EUR][1000 genomes]
rs3095235	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3115536	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3115537	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130051	0.83[EUR][1000 genomes]
rs3130052	0.81[EUR][1000 genomes]
rs3130054	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130056	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130057	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130058	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130638	0.81[EUR][1000 genomes]
rs3130640	0.87[EUR][1000 genomes]
rs3131628	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131629	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3131630	0.90[ASN][1000 genomes]
rs3131633	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3132458	0.86[EUR][1000 genomes]
rs3132461	0.86[EUR][1000 genomes]
rs9267485	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
2	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
3	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
4	esv3381377	chr6:31192213-31498578	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
5	esv3340592	chr6:31192248-31498535	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
6	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
7	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
8	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
9	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
10	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
11	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
12	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
13	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
14	nsv1018463	chr6:31337336-31525275	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
15	nsv538189	chr6:31337336-31525275	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
16	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
17	esv2752115	chr6:31352880-31498721	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
18	esv2757162	chr6:31353329-31542308	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
19	esv2752119	chr6:31359621-31498521	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
20	nsv432874	chr6:31379821-31498521	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
21	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
22	nsv432877	chr6:31412961-31528690	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
23	nsv1021578	chr6:31448533-31498737	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
24	nsv884414	chr6:31458633-31498497	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
25	nsv884415	chr6:31458633-31501413	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
26	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
27	nsv470809	chr6:31496915-31544189	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3093978	HLA-F	cis	multi-tissue	Pritchard
rs3093978	HLA-DRB5	cis	multi-tissue	Pritchard
rs3093978	HCG27	cis	multi-tissue	Pritchard
rs3093978	HLA-DRB5	cis	lymphoblastoid	GTEx
rs3093978	HIST1H1B	cis	cerebellum	SCAN
rs3093978	HLA-DRB1	cis	multi-tissue	Pritchard
rs3093978	HLA-C	cis	lymphoblastoid	GTEx
rs3093978	HCG22	cis	lymphoblastoid	seeQTL
rs3093978	HLA-C	cis	multi-tissue	Pritchard
rs3093978	HLA-DRB5	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31467400-31506600	Weak transcription	Right Atrium	heart
2	chr6:31495800-31506200	Strong transcription	Thymus	Thymus
3	chr6:31496000-31502000	Weak transcription	Psoas Muscle	Psoas
4	chr6:31496000-31506200	Strong transcription	Fetal Brain Female	brain
5	chr6:31496200-31498800	Weak transcription	Fetal Heart	heart
6	chr6:31496200-31506400	Strong transcription	Fetal Stomach	stomach
7	chr6:31496200-31506800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:31496400-31503400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:31496400-31505600	Strong transcription	Fetal Thymus	thymus
10	chr6:31496400-31506000	Strong transcription	Brain Germinal Matrix	brain
11	chr6:31496800-31498800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:31496800-31505800	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr6:31496800-31506400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:31496800-31506400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:31496800-31506400	Strong transcription	Gastric	stomach
16	chr6:31496800-31506600	Strong transcription	Brain Cingulate Gyrus	brain
17	chr6:31496800-31507800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:31497000-31502200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:31497000-31502600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr6:31497000-31506200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:31497000-31506400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:31497000-31506400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:31497200-31500200	Strong transcription	Right Ventricle	heart
24	chr6:31497200-31503200	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr6:31497200-31503800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr6:31497200-31504800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:31497200-31505200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr6:31497200-31505600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:31497200-31506000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:31497200-31506000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:31497200-31506000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr6:31497200-31506000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr6:31497200-31506400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:31497200-31506600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:31497200-31506600	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr6:31497200-31506600	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr6:31497200-31506600	Strong transcription	A549	lung
38	chr6:31497200-31506600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr6:31497200-31506800	Strong transcription	Rectal Smooth Muscle	rectum
40	chr6:31497400-31498600	Genic enhancers	Liver	Liver
41	chr6:31497400-31498800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:31497400-31499400	Strong transcription	Spleen	Spleen
43	chr6:31497400-31503600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:31497400-31503800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr6:31497400-31504000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:31497400-31504800	Strong transcription	Brain Hippocampus Middle	brain
47	chr6:31497400-31505000	Strong transcription	Ovary	ovary
48	chr6:31497400-31505800	Strong transcription	Primary T cells from cord blood	blood
49	chr6:31497400-31506000	Strong transcription	Brain Anterior Caudate	brain
50	chr6:31497400-31506000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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