Variant report

Variant	rs12119232
Chromosome Location	chr1:171711152-171711153
allele	A/C
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:171710699..171711209-chr3:15643168..15644027,2	Hela-S3	cervix:
2	chr1:171711054..171711741-chr12:92539162..92539700,2	Hela-S3	cervix:
3	chr1:171711044..171711901-chr12:56552077..56552933,3	Hela-S3	cervix:
4	chr1:171710341..171715416-chr1:171748571..171752440,7	MCF-7	breast:
5	chr1:171708496..171713095-chr1:171747641..171752422,13	MCF-7	breast:
6	chr1:171453211..171456610-chr1:171708836..171712780,4	K562	blood:
7	chr1:171709343..171715185-chr1:171748592..171756289,15	K562	blood:
8	chr1:171710254..171714548-chr1:171728803..171733052,4	K562	blood:
9	chr1:171711105..171711830-chr19:1747797..1748306,2	Hela-S3	cervix:
10	chr1:171710837..171713389-chr1:171720682..171723071,4	K562	blood:
11	chr1:171709554..171712819-chr1:171724332..171729197,5	K562	blood:
12	chr1:171710699..171713555-chr1:171719677..171724483,6	MCF-7	breast:
13	chr1:171710037..171714996-chr1:171734843..171738629,6	MCF-7	breast:
14	chr1:171614558..171616177-chr1:171708966..171711154,2	MCF-7	breast:
15	chr1:171709564..171713750-chr1:171736602..171743117,7	K562	blood:
16	chr1:171711038..171711726-chr20:62496460..62497159,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000169814	Chromatin interaction
ENSG00000232261	Chromatin interaction
ENSG00000010165	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000131373	Chromatin interaction
ENSG00000271459	Chromatin interaction
ENSG00000133639	Chromatin interaction
ENSG00000253060	Chromatin interaction
ENSG00000101150	Chromatin interaction
ENSG00000245904	Chromatin interaction
ENSG00000117523	Chromatin interaction
ENSG00000236741	Chromatin interaction
ENSG00000267073	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1001373	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10489249	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10489251	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1052676	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10753181	0.94[ASN][1000 genomes]
rs10903	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10913489	0.82[EUR][1000 genomes]
rs10913490	0.82[EUR][1000 genomes]
rs10913492	0.82[EUR][1000 genomes]
rs10913511	0.93[EUR][1000 genomes]
rs10913514	0.93[EUR][1000 genomes]
rs10913529	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10913565	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10913578	0.94[ASN][1000 genomes]
rs10913582	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10913587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11576221	0.82[EUR][1000 genomes]
rs11577073	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11577197	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11577745	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11578179	0.93[EUR][1000 genomes]
rs11578699	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11578723	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11579698	0.94[EUR][1000 genomes]
rs11580415	0.94[EUR][1000 genomes]
rs11580522	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11583920	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11590680	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11590714	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11799420	0.82[EUR][1000 genomes]
rs11801846	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11803174	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11808099	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11811780	0.83[EUR][1000 genomes]
rs12123727	0.81[EUR][1000 genomes]
rs12126566	0.86[ASN][1000 genomes]
rs12127026	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12128536	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12132221	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs15655	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16843230	0.92[ASN][1000 genomes]
rs16843251	0.92[ASN][1000 genomes]
rs17649050	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17649068	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2298914	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2421911	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3753539	0.94[ASN][1000 genomes]
rs3766653	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55670848	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58455759	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6656003	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6659874	0.82[EUR][1000 genomes]
rs6667559	0.82[EUR][1000 genomes]
rs6669263	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6678890	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6679354	0.94[EUR][1000 genomes]
rs7528057	0.81[EUR][1000 genomes]
rs7536436	0.94[EUR][1000 genomes]
rs7536543	0.94[EUR][1000 genomes]
rs9661596	0.82[EUR][1000 genomes]
rs9662853	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12119232	VAMP4	Cis_1M	lymphoblastoid	RTeQTL
rs12119232	VAMP4	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171708800-171712600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:171708800-171712800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:171709200-171712200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:171709200-171712400	Active TSS	NHLF	lung
5	chr1:171709400-171712400	Active TSS	NHDF-Ad	bronchial
6	chr1:171709400-171712600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:171709800-171712400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:171709800-171712600	Active TSS	Aorta	Aorta
9	chr1:171709800-171712600	Active TSS	Psoas Muscle	Psoas
10	chr1:171710000-171711800	Active TSS	Primary T cells fromperipheralblood	blood
11	chr1:171710000-171712000	Active TSS	Brain Angular Gyrus	brain
12	chr1:171710000-171712400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:171710000-171712600	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr1:171710000-171712600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:171710000-171712600	Active TSS	Stomach Smooth Muscle	stomach
16	chr1:171710000-171713000	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr1:171710000-171713000	Active TSS	Fetal Brain Male	brain
18	chr1:171710200-171712000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:171710200-171712000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr1:171710200-171712000	Active TSS	Left Ventricle	heart
21	chr1:171710200-171712000	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr1:171710200-171712000	Active TSS	Stomach Mucosa	stomach
23	chr1:171710200-171712000	Active TSS	HSMM	muscle
24	chr1:171710200-171712200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr1:171710200-171712200	Active TSS	H9 Cell Line	embryonic stem cell
26	chr1:171710200-171712200	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr1:171710200-171712200	Active TSS	Fetal Intestine Large	intestine
28	chr1:171710200-171712200	Active TSS	Fetal Stomach	stomach
29	chr1:171710200-171712200	Active TSS	Ovary	ovary
30	chr1:171710200-171712400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:171710200-171712400	Active TSS	Colon Smooth Muscle	Colon
32	chr1:171710200-171712400	Active TSS	Thymus	Thymus
33	chr1:171710200-171712600	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr1:171710200-171712800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:171710200-171712800	Active TSS	Fetal Muscle Trunk	muscle
36	chr1:171710200-171713000	Active TSS	Right Ventricle	heart
37	chr1:171710400-171711600	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr1:171710400-171711600	Active TSS	Placenta	Placenta
39	chr1:171710400-171711800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:171710400-171711800	Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr1:171710400-171711800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:171710400-171712000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:171710400-171712000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:171710400-171712000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:171710400-171712000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:171710400-171712000	Active TSS	Esophagus	oesophagus
47	chr1:171710400-171712000	Active TSS	Fetal Intestine Small	intestine
48	chr1:171710400-171712000	Active TSS	Gastric	stomach
49	chr1:171710400-171712000	Active TSS	Lung	lung
50	chr1:171710400-171712000	Active TSS	Pancreas	Pancrea

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