Variant report

Variant	rs3901749
Chromosome Location	chr9:15279280-15279281
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:15275279..15280411-chr9:15305554..15308797,6	MCF-7	breast:
2	chr9:15278015..15280577-chr9:15305865..15308821,3	MCF-7	breast:
3	chr9:15277682..15279519-chr9:15415467..15418240,3	MCF-7	breast:
4	chr9:15276823..15279769-chr9:15280291..15283089,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155158	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10120504	1.00[JPT][hapmap]
rs10121394	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10122040	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10122202	1.00[JPT][hapmap]
rs10125329	1.00[JPT][hapmap]
rs10810369	1.00[JPT][hapmap]
rs10961950	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10961951	0.88[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10961955	1.00[JPT][hapmap]
rs12003180	1.00[JPT][hapmap]
rs12349572	0.94[ASW][hapmap];0.87[TSI][hapmap]
rs12349889	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1475229	1.00[JPT][hapmap]
rs2616751	1.00[JPT][hapmap]
rs3853430	0.88[CHB][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3853431	1.00[ASW][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3853432	0.85[CHB][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3933784	1.00[JPT][hapmap]
rs3933785	1.00[JPT][hapmap]
rs4237138	1.00[JPT][hapmap]
rs471364	1.00[JPT][hapmap]
rs578194	1.00[JPT][hapmap]
rs612183	0.82[JPT][hapmap]
rs643531	1.00[JPT][hapmap]
rs660686	1.00[JPT][hapmap]
rs661048	1.00[JPT][hapmap]
rs675849	1.00[JPT][hapmap]
rs686030	1.00[JPT][hapmap]
rs7035671	0.82[JPT][hapmap]
rs7035801	0.82[JPT][hapmap]
rs7037559	1.00[JPT][hapmap]
rs7855226	0.82[TSI][hapmap]
rs7862255	0.82[AFR][1000 genomes]
rs7873299	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7873760	0.87[ASW][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7874222	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs912280	0.81[AFR][1000 genomes]
rs9657588	1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031340	chr9:15163004-15332769	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2761505	chr9:15274373-15319613	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15241200-15286200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr9:15243000-15293400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr9:15250200-15288200	Weak transcription	Fetal Stomach	stomach
4	chr9:15253800-15286400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr9:15254000-15293000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:15254200-15293000	Weak transcription	NHEK	skin
7	chr9:15254200-15295600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:15259200-15293400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr9:15260600-15283000	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:15263800-15283000	Weak transcription	Aorta	Aorta
11	chr9:15264200-15285800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:15273600-15286000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr9:15273600-15293400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr9:15273800-15280200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr9:15273800-15282800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr9:15274000-15286000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr9:15274000-15288400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:15274000-15288400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:15274400-15279400	Weak transcription	Primary T cells from cord blood	blood
20	chr9:15274600-15281200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:15274600-15281800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:15274800-15280600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr9:15275000-15280200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr9:15275000-15280600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr9:15275400-15280600	Enhancers	HepG2	liver
26	chr9:15276800-15284800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:15277000-15292200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr9:15277000-15293000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:15277600-15279400	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr9:15277600-15280400	Enhancers	Liver	Liver
31	chr9:15277600-15288400	Weak transcription	Lung	lung
32	chr9:15277600-15296800	Weak transcription	Gastric	stomach
33	chr9:15278000-15286000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr9:15278000-15286200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr9:15278000-15295200	Weak transcription	Pancreas	Pancrea
36	chr9:15278200-15282800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr9:15278200-15283000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr9:15278200-15289400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr9:15278600-15279800	Enhancers	Fetal Intestine Large	intestine
40	chr9:15278600-15282600	Weak transcription	Stomach Mucosa	stomach
41	chr9:15278600-15286200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr9:15278600-15291200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:15278800-15279400	Weak transcription	Fetal Kidney	kidney
44	chr9:15278800-15279600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr9:15279200-15279600	Enhancers	Primary B cells from peripheral blood	blood
46	chr9:15279200-15279600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr9:15279200-15279600	Enhancers	Ovary	ovary
48	chr9:15279200-15279600	Enhancers	Small Intestine	intestine
49	chr9:15279200-15279800	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr9:15279200-15279800	Enhancers	Fetal Intestine Small	intestine

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