Variant report

Variant	rs3093974
Chromosome Location	chr6:31506210-31506211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31506210-31506315	K562	blood:	n/a	n/a
2	POLR2A	chr6:31505570-31507667	K562	blood:	n/a	n/a
3	POLR2A	chr6:31505026-31508472	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:31505301-31507731	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr6:31506161-31507185	MCF-7	breast:	n/a	n/a
6	POLR2A	chr6:31505967-31506971	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr6:31505312-31508500	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:31505892-31507329	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr6:31505947-31507121	GM12892	blood:	n/a	n/a
10	POLR2A	chr6:31505860-31506320	K562	blood:	n/a	n/a
11	POLR2A	chr6:31506089-31508478	HepG2	liver:	n/a	n/a
12	POLR2A	chr6:31505934-31507183	GM12892	blood:	n/a	n/a
13	POLR2A	chr6:31505922-31506282	H1-hESC	embryonic stem cell:	n/a	n/a
14	HEY1	chr6:31506024-31508418	K562	blood:	n/a	n/a
15	POLR2A	chr6:31505819-31511508	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr6:31505978-31506324	GM12891	blood:	n/a	n/a
17	POLR2A	chr6:31505627-31507017	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:31505940-31506260	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:31459710..31467567-chr6:31506191..31511027,18	MCF-7	breast:
2	chr6:31504619..31508588-chr6:31538806..31541615,4	K562	blood:
3	chr6:31458384..31468965-chr6:31503613..31512721,28	K562	blood:
4	chr6:31505275..31506806-chr6:31571359..31573791,2	K562	blood:
5	chr6:31505350..31512312-chr6:31630543..31635379,11	K562	blood:
6	chr6:31505549..31508168-chr6:31560722..31562471,2	K562	blood:
7	chr6:31506029..31511048-chr6:31626239..31630287,7	MCF-7	breast:
8	chr6:31460486..31468205-chr6:31503942..31512721,23	K562	blood:
9	chr6:31504619..31510971-chr6:31539361..31543067,6	K562	blood:

No data

Variant related genes	Relation type
DDX39B-AS1	TF binding region
DDX39B	TF binding region
SNORD117	TF binding region
ENSG00000204475	Chromatin interaction
ENSG00000263020	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000201680	Chromatin interaction
ENSG00000226979	Chromatin interaction
ENSG00000204439	Chromatin interaction
ENSG00000204516	Chromatin interaction
ENSG00000201207	Chromatin interaction
ENSG00000204435	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1041981	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11796	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1800683	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2071591	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2071592	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2071594	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3093949	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3093987	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3094594	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3130059	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3130629	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3131641	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3132455	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs909253	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3093974	PACSIN1	cis	parietal	SCAN
rs3093974	CSNK2B	cis	lymphoblastoid	seeQTL
rs3093974	ZKSCAN4	cis	parietal	SCAN
rs3093974	ZNF165	cis	parietal	SCAN
rs3093974	DEF6	cis	parietal	SCAN
rs3093974	HLA-DQA1	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	chr6:31496200-31506400	Strong transcription	Fetal Stomach	stomach
3	chr6:31496200-31506800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:31496800-31506400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:31496800-31506400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:31496800-31506400	Strong transcription	Gastric	stomach
7	chr6:31496800-31506600	Strong transcription	Brain Cingulate Gyrus	brain
8	chr6:31496800-31507800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:31497000-31506400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr6:31497000-31506400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:31497200-31506400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:31497200-31506600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:31497200-31506600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr6:31497200-31506600	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr6:31497200-31506600	Strong transcription	A549	lung
16	chr6:31497200-31506600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr6:31497200-31506800	Strong transcription	Rectal Smooth Muscle	rectum
18	chr6:31497400-31506400	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr6:31497400-31506400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:31497400-31506400	Strong transcription	Adipose Nuclei	Adipose
21	chr6:31497400-31506400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:31497400-31506400	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:31497400-31506400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr6:31497400-31506400	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:31497400-31506600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:31497400-31506600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:31497400-31506600	Strong transcription	Placenta	Placenta
28	chr6:31497400-31506600	Strong transcription	NHLF	lung
29	chr6:31497400-31506800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:31497400-31506800	Strong transcription	Colonic Mucosa	Colon
31	chr6:31497400-31506800	Strong transcription	Esophagus	oesophagus
32	chr6:31497400-31506800	Strong transcription	Lung	lung
33	chr6:31497400-31506800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr6:31497600-31506400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:31497600-31506400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr6:31497600-31506400	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr6:31497600-31506400	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr6:31497600-31506800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr6:31497600-31506800	Strong transcription	Left Ventricle	heart
40	chr6:31497600-31507200	Strong transcription	HSMMtube	muscle
41	chr6:31497600-31507600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:31497600-31508000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:31497800-31506400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:31497800-31506400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:31497800-31506400	Strong transcription	HMEC	breast
46	chr6:31497800-31506400	Strong transcription	HSMM	muscle
47	chr6:31497800-31506400	Strong transcription	NHDF-Ad	bronchial
48	chr6:31497800-31506600	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:31497800-31506600	Strong transcription	Aorta	Aorta
50	chr6:31497800-31506800	Strong transcription	H1 Cell Line	embryonic stem cell

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