Variant report

Variant	rs3736836
Chromosome Location	chr9:95060630-95060631
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr9:95060444-95061015	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr9:95060484-95060683	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:95058975..95061785-chr9:95061896..95063797,3	MCF-7	breast:
2	chr9:95058426..95060967-chr9:95080944..95083546,2	MCF-7	breast:
3	chr9:95051112..95065542-chr9:95079443..95091389,38	K562	blood:
4	chr9:95052930..95062724-chr9:95083607..95090664,16	MCF-7	breast:
5	chr9:95036194..95038601-chr9:95058993..95061948,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IARS-1	chr9:95060539-95061236	NONHSAT133187

No data

Variant related genes	Relation type
IARS	TF binding region
ENSG00000198000	Chromatin interaction
ENSG00000188312	Chromatin interaction

Extended variants
information (count: 154 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs15717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908281	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17518691	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17518754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17519320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs17519397	0.88[EUR][1000 genomes]
rs17519453	0.83[EUR][1000 genomes]
rs17519719	1.00[CHB][hapmap]
rs17590748	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17591007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17591372	0.88[EUR][1000 genomes]
rs17591776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17592026	1.00[AMR][1000 genomes]
rs17677599	0.90[ASN][1000 genomes]
rs17678735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044540	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2230405	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2236343	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2236344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2273860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2274967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28365880	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34860658	0.83[EUR][1000 genomes]
rs3736834	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737147	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3758228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs3758230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758231	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758232	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3780342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3780348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3858097	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs41276835	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41277647	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41277739	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41278699	1.00[AMR][1000 genomes]
rs41280223	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41297183	1.00[EUR][1000 genomes]
rs41301527	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs41307467	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41312230	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4298540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59083571	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59627747	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61742574	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67546506	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72750403	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750404	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750405	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750407	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750408	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750409	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750418	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750419	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750420	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750421	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750422	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750426	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750427	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750430	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750431	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750432	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750433	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750434	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750437	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750438	0.83[EUR][1000 genomes]
rs72750441	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750445	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750447	1.00[ASN][1000 genomes]
rs72750448	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750449	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750450	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750451	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750454	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750456	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750457	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750458	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750460	1.00[AMR][1000 genomes]
rs72750463	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750465	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750466	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750468	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750469	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750472	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750474	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750477	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750478	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750479	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750482	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750483	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750487	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750490	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750491	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750493	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750494	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750496	0.94[EUR][1000 genomes]
rs72750498	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750499	0.90[AMR][1000 genomes]
rs72750500	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72750501	1.00[EUR][1000 genomes]
rs72750502	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72752403	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72752404	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72752405	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72752406	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72752411	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72752417	0.94[EUR][1000 genomes]
rs72752419	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72752422	0.94[EUR][1000 genomes]
rs72752425	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72752427	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72752431	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72752435	0.94[EUR][1000 genomes]
rs72752442	1.00[EUR][1000 genomes]
rs72752443	1.00[EUR][1000 genomes]
rs72752444	1.00[EUR][1000 genomes]
rs72752445	1.00[EUR][1000 genomes]
rs72752446	1.00[EUR][1000 genomes]
rs72752449	1.00[EUR][1000 genomes]
rs72752453	1.00[EUR][1000 genomes]
rs72752454	1.00[EUR][1000 genomes]
rs72752457	1.00[EUR][1000 genomes]
rs72752458	1.00[EUR][1000 genomes]
rs72752460	1.00[EUR][1000 genomes]
rs72752463	1.00[EUR][1000 genomes]
rs72752467	0.83[EUR][1000 genomes]
rs72752471	0.88[EUR][1000 genomes]
rs72752472	0.88[EUR][1000 genomes]
rs72752474	0.83[EUR][1000 genomes]
rs72752475	0.88[EUR][1000 genomes]
rs72752477	0.88[EUR][1000 genomes]
rs72752479	0.88[EUR][1000 genomes]
rs72752482	0.88[EUR][1000 genomes]
rs72752483	0.88[EUR][1000 genomes]
rs72752484	0.88[EUR][1000 genomes]
rs72752485	0.88[EUR][1000 genomes]
rs72752486	0.88[EUR][1000 genomes]
rs72752492	0.88[EUR][1000 genomes]
rs72752493	0.88[EUR][1000 genomes]
rs72752497	0.88[EUR][1000 genomes]
rs72754412	1.00[AMR][1000 genomes]
rs7872423	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs921122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS 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 miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer 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	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active 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	45 gene(s)	inside rSNPs	diseases
6	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1045165	chr9:95057462-95138564	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3736836	GPER	trans	lymphoblastoid	seeQTL
rs3736836	IL13RA1	trans	lymphoblastoid	seeQTL
rs3736836	WNT5A	trans	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95056800-95086800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:95057000-95060800	Weak transcription	Colonic Mucosa	Colon
3	chr9:95057000-95061000	Weak transcription	Thymus	Thymus
4	chr9:95057000-95061400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:95057000-95061400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:95057000-95061400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:95057000-95061400	Weak transcription	Lung	lung
8	chr9:95057000-95061400	Weak transcription	Spleen	Spleen
9	chr9:95057000-95064800	Weak transcription	Ovary	ovary
10	chr9:95057000-95065000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:95057000-95070400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:95057000-95072600	Weak transcription	Gastric	stomach
13	chr9:95057000-95087000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:95057200-95061000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:95057200-95061400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr9:95057200-95061400	Weak transcription	Brain Angular Gyrus	brain
17	chr9:95057200-95063400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:95057200-95069000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr9:95057400-95061000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr9:95057400-95063200	Weak transcription	Fetal Brain Male	brain
21	chr9:95057400-95064600	Weak transcription	Right Ventricle	heart
22	chr9:95057400-95071200	Weak transcription	Small Intestine	intestine
23	chr9:95057800-95061400	Weak transcription	Pancreas	Pancrea
24	chr9:95057800-95063200	Weak transcription	Psoas Muscle	Psoas
25	chr9:95058000-95086200	Weak transcription	Stomach Mucosa	stomach
26	chr9:95058200-95061400	Weak transcription	Fetal Intestine Small	intestine
27	chr9:95058200-95073600	Strong transcription	Stomach Smooth Muscle	stomach
28	chr9:95058200-95073600	Strong transcription	HUVEC	blood vessel
29	chr9:95058200-95074600	Strong transcription	Fetal Thymus	thymus
30	chr9:95058200-95074800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr9:95058200-95085800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr9:95058400-95073400	Strong transcription	Fetal Lung	lung
33	chr9:95058400-95073600	Strong transcription	HMEC	breast
34	chr9:95058400-95074200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr9:95058400-95074800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:95058400-95085600	Strong transcription	Placenta	Placenta
37	chr9:95058400-95085800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:95058400-95085800	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr9:95058400-95086200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:95058600-95061200	Strong transcription	Primary B cells from cord blood	blood
41	chr9:95058600-95071000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:95058600-95071200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr9:95058600-95073800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr9:95058600-95085800	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr9:95058600-95085800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr9:95058800-95067600	Weak transcription	Fetal Heart	heart
47	chr9:95058800-95073600	Strong transcription	NHDF-Ad	bronchial
48	chr9:95058800-95073800	Strong transcription	Dnd41	blood
49	chr9:95059000-95061000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr9:95059000-95062400	Strong transcription	Brain Inferior Temporal Lobe	brain

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