Variant report

Variant	rs2516390
Chromosome Location	chr6:31529883-31529884
allele	A/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31529683..31532645-chr6:31541228..31544283,3	K562	blood:
2	chr6:31527419..31530121-chr6:31566009..31569893,3	K562	blood:
3	chr6:31507117..31518882-chr6:31523749..31531427,29	K562	blood:
4	chr6:31528630..31531366-chr6:31743392..31745333,2	K562	blood:
5	chr6:31526758..31532788-chr6:31533564..31537563,8	K562	blood:
6	chr6:31529623..31531832-chr6:31546596..31549041,2	K562	blood:
7	chr6:31529234..31533520-chr6:31586129..31590672,6	K562	blood:
8	chr6:31519386..31522275-chr6:31529123..31531793,2	K562	blood:
9	chr6:31526758..31530982-chr6:31533053..31538001,9	K562	blood:
10	chr6:31529423..31531905-chr6:31555103..31557891,2	MCF-7	breast:
11	chr6:31527769..31531613-chr6:31630147..31633759,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204482	Chromatin interaction
ENSG00000254870	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000265236	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000232810	Chromatin interaction
ENSG00000234006	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000201207	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000204396	Chromatin interaction
ENSG00000204498	Chromatin interaction
ENSG00000213760	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1121800	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239704	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2516391	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516479	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523500	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2844483	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844484	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844485	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2844486	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857602	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857710	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3094595	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3135042	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3135043	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746868	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs928815	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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
13	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
14	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
15	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
16	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
17	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
18	nsv462870	chr6:31528130-31544189	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
19	nsv601941	chr6:31528130-31544189	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2516390	HLA-DRB5	cis	lymphoblastoid	GTEx
rs2516390	HLA-DRB5	cis	parietal	SCAN
rs2516390	DEF6	cis	parietal	SCAN
rs2516390	BAT1	cis	multi-tissue	Pritchard
rs2516390	HIST1H1B	cis	cerebellum	SCAN
rs2516390	HIST1H3I	cis	cerebellum	SCAN
rs2516390	TEAD3	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31516000-31535800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr6:31516400-31533200	Weak transcription	Fetal Brain Male	brain
3	chr6:31516800-31530800	Weak transcription	Stomach Mucosa	stomach
4	chr6:31516800-31531000	Weak transcription	Fetal Kidney	kidney
5	chr6:31526400-31532600	Weak transcription	Fetal Lung	lung
6	chr6:31526800-31530200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:31527200-31530000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:31527400-31535400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:31527400-31535400	Weak transcription	HepG2	liver
10	chr6:31527800-31530000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr6:31527800-31530400	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr6:31528000-31530000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr6:31528000-31532000	Enhancers	Spleen	Spleen
14	chr6:31528000-31535200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:31528200-31531600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:31528200-31532000	Enhancers	Primary hematopoietic stem cells	blood
17	chr6:31528200-31532000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:31528200-31532000	Enhancers	HUVEC	blood vessel
19	chr6:31528200-31535600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:31528400-31530400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:31528400-31530600	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr6:31528400-31530800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:31528400-31530800	Weak transcription	Aorta	Aorta
24	chr6:31528400-31531200	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr6:31528400-31531200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr6:31528400-31531600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:31528400-31535400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr6:31528600-31530600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:31528600-31531000	Weak transcription	NHLF	lung
30	chr6:31528600-31532000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:31528600-31532200	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr6:31528600-31535600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:31528600-31541200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:31528800-31530400	Genic enhancers	Primary T cells fromperipheralblood	blood
35	chr6:31528800-31530400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:31528800-31530800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:31528800-31531200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:31528800-31531800	Enhancers	Primary B cells from peripheral blood	blood
39	chr6:31528800-31532000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr6:31528800-31532000	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr6:31528800-31535600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:31529000-31530400	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr6:31529000-31530400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:31529000-31530400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:31529000-31530800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:31529000-31530800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:31529000-31530800	Weak transcription	HSMMtube	muscle
48	chr6:31529000-31531000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:31529000-31531000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:31529000-31531000	Weak transcription	Rectal Mucosa Donor 29	rectum

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