Variant report

Variant	rs1476331
Chromosome Location	chr3:195959924-195959925
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr3:195959227-195960165	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:195959904-195959980	HUVEC	blood vessel:	n/a	n/a
3	MTA3	chr3:195959116-195960078	GM12878	blood:	n/a	n/a
4	STAT5A	chr3:195959262-195959996	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:195959778-195960836	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr3:195959734-195960865	HepG2	liver:	n/a	n/a
7	PML	chr3:195959228-195960098	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:195958699-195960775	K562	blood:	n/a	n/a
9	IKZF1	chr3:195959382-195960071	GM12878	blood:	n/a	n/a
10	RELA	chr3:195959324-195960086	GM12891	blood:	n/a	n/a
11	POLR2A	chr3:195959895-195960330	U87	brain:	n/a	n/a
12	RUNX3	chr3:195959356-195960226	GM12878	blood:	n/a	n/a
13	IRF4	chr3:195959307-195960188	GM12878	blood:	n/a	n/a
14	WRNIP1	chr3:195959400-195960140	GM12878	blood:	n/a	n/a
15	SPI1	chr3:195959126-195960080	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:195959590-195960026	GM12878	blood:	n/a	n/a
17	RUNX3	chr3:195959328-195960199	GM12878	blood:	n/a	n/a
18	BATF	chr3:195959765-195960161	GM12878	blood:	n/a	n/a
19	STAT1	chr3:195959834-195959965	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:195959650-195960475	HepG2	liver:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:195958884..195960424-chr3:195972113..195974415,2	K562	blood:
2	chr3:195952367..195954245-chr3:195957237..195960071,2	K562	blood:

No data

Variant related genes	Relation type
SLC51A	TF binding region
ENSG00000161217	Chromatin interaction
ENSG00000163959	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12491227	0.96[CEU][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12630070	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs1476332	0.96[CEU][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17852687	1.00[CEU][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4916440	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4916441	0.81[ASN][1000 genomes]
rs4916531	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58021463	0.86[ASN][1000 genomes]
rs67723323	0.82[ASN][1000 genomes]
rs6807596	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs68119320	0.86[ASN][1000 genomes]
rs712012	0.81[ASN][1000 genomes]
rs7625886	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs7639752	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.82[ASN][1000 genomes]
rs870339	0.85[JPT][hapmap]
rs9343	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs939883	0.81[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv878171	chr3:195677895-195959924	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv1008512	chr3:195709662-195974936	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
8	nsv1009105	chr3:195769609-195984388	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
10	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
11	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
13	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
14	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
15	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
16	nsv878175	chr3:195907653-195973244	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	nsv1014159	chr3:195908999-195968512	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
18	nsv878176	chr3:195926234-195959924	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv878178	chr3:195929268-195998451	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
20	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
21	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
22	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
23	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1476331	SLC51A	cis	Esophagus Muscularis	GTEx
rs1476331	SLC51A	cis	Artery Tibial	GTEx
rs1476331	SLC51A	cis	Adipose Subcutaneous	GTEx
rs1476331	PCYT1A	Cis_1M	lymphoblastoid	RTeQTL
rs1476331	PCYT1A	cis	Liver	GTEx
rs1476331	SLC51A	cis	Muscle Skeletal	GTEx
rs1476331	PCYT1A	cis	multi-tissue	Pritchard

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195944200-195964000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:195945000-195968400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:195946600-195965600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:195946800-195962600	Weak transcription	Primary T cells from cord blood	blood
5	chr3:195946800-195964200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:195946800-195967400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:195947000-195960800	Weak transcription	Fetal Intestine Large	intestine
8	chr3:195947000-195963800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:195947000-195964000	Weak transcription	Colonic Mucosa	Colon
10	chr3:195947200-195962000	Weak transcription	Fetal Brain Male	brain
11	chr3:195947200-195962600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:195947200-195962600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:195948000-195970400	Strong transcription	Liver	Liver
14	chr3:195950400-195964400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:195952600-195963200	Weak transcription	K562	blood
16	chr3:195953200-195963800	Weak transcription	Brain Germinal Matrix	brain
17	chr3:195954600-195960000	Weak transcription	Fetal Brain Female	brain
18	chr3:195954600-195960400	Weak transcription	Lung	lung
19	chr3:195954600-195962200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:195954600-195963800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:195954600-195964600	Weak transcription	Brain Angular Gyrus	brain
22	chr3:195954600-195964800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:195954800-195962800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:195954800-195963800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:195954800-195963800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:195954800-195963800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr3:195954800-195964600	Weak transcription	NHDF-Ad	bronchial
28	chr3:195954800-195968600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:195955000-195963000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:195955000-195963200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:195955000-195963800	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:195955000-195963800	Weak transcription	HMEC	breast
33	chr3:195955000-195964000	Weak transcription	Fetal Lung	lung
34	chr3:195955200-195961000	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:195955200-195963000	Weak transcription	Spleen	Spleen
36	chr3:195955200-195963200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:195955200-195964200	Weak transcription	HSMM	muscle
38	chr3:195955400-195963600	Weak transcription	Gastric	stomach
39	chr3:195955400-195964000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:195955400-195968400	Weak transcription	Pancreas	Pancrea
41	chr3:195955600-195962200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:195955600-195963000	Weak transcription	Left Ventricle	heart
43	chr3:195955600-195963600	Weak transcription	Right Ventricle	heart
44	chr3:195955600-195964200	Weak transcription	HSMMtube	muscle
45	chr3:195956000-195961200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:195956000-195962800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr3:195956000-195963800	Weak transcription	Placenta	Placenta
48	chr3:195956000-195969800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:195956400-195963600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:195956800-195960000	Weak transcription	Ovary	ovary

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