Variant report

Variant	rs9657894
Chromosome Location	chr7:150437927-150437928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:150433868..150435484-chr7:150436619..150439022,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196329	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10239400	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10242011	0.86[ASN][1000 genomes]
rs10271868	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1046355	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11760839	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12703098	0.86[ASN][1000 genomes]
rs17173582	0.82[JPT][hapmap]
rs2286898	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286899	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs28418764	0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs28505524	0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs28641865	0.92[ASN][1000 genomes]
rs34078863	0.86[ASN][1000 genomes]
rs34443555	0.87[ASN][1000 genomes]
rs34906783	0.85[ASN][1000 genomes]
rs35112724	0.80[ASN][1000 genomes]
rs35257925	0.83[ASN][1000 genomes]
rs4725937	0.81[ASN][1000 genomes]
rs57024360	0.84[ASN][1000 genomes]
rs62490401	0.80[ASN][1000 genomes]
rs62490403	0.80[ASN][1000 genomes]
rs6598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6980405	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs759011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7807580	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9657886	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9657890	0.95[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9657898	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9657900	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9969148	0.85[ASN][1000 genomes]
rs9969242	0.86[ASN][1000 genomes]
rs9969243	0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9969309	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	esv2758617	chr7:150251949-150463804	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2759573	chr7:150251949-150463804	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv967475	chr7:150323577-150610034	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv831187	chr7:150325913-150503500	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9657894	RP5-1051J4.4	cis	lung	GTEx
rs9657894	RP5-1051J4.4	cis	Whole Blood	GTEx
rs9657894	RP5-1051J4.4	cis	Thyroid	GTEx
rs9657894	GIMAP5	cis	normal skin	skin_eQTL
rs9657894	GIMAP8	cis	parietal	SCAN
rs9657894	RP5-1051J4.4	cis	Adipose Subcutaneous	GTEx
rs9657894	GIMAP5	cis	uninvolved skin	skin_eQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150433800-150439200	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr7:150434000-150438000	Active TSS	Right Atrium	heart
3	chr7:150434200-150438000	Active TSS	Duodenum Mucosa	Duodenum
4	chr7:150434200-150438000	Active TSS	Psoas Muscle	Psoas
5	chr7:150434600-150440600	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr7:150435400-150439000	Active TSS	GM12878-XiMat	blood
7	chr7:150435400-150442800	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
8	chr7:150435600-150442400	Weak transcription	Ovary	ovary
9	chr7:150435800-150439600	Weak transcription	Colon Smooth Muscle	Colon
10	chr7:150435800-150441000	Weak transcription	Pancreas	Pancrea
11	chr7:150435800-150441200	Weak transcription	Gastric	stomach
12	chr7:150435800-150441800	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
13	chr7:150436000-150441800	Weak transcription	Fetal Intestine Small	intestine
14	chr7:150436200-150439600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr7:150436200-150450200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:150436400-150439600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr7:150436400-150443400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
18	chr7:150436800-150438000	Weak transcription	Placenta	Placenta
19	chr7:150436800-150438200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr7:150436800-150442200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
21	chr7:150436800-150451400	Weak transcription	Brain Substantia Nigra	brain
22	chr7:150437000-150438000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:150437000-150439800	Weak transcription	Fetal Heart	heart
24	chr7:150437000-150441600	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
25	chr7:150437000-150450000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr7:150437200-150438200	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:150437200-150441400	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
28	chr7:150437200-150441600	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr7:150437200-150441600	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
30	chr7:150437200-150442400	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
31	chr7:150437200-150442400	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
32	chr7:150437200-150442600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:150437200-150443200	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
34	chr7:150437400-150439600	Strong transcription	Fetal Thymus	thymus
35	chr7:150437400-150441400	Weak transcription	Colonic Mucosa	Colon
36	chr7:150437400-150441800	Weak transcription	Thymus	Thymus
37	chr7:150437400-150443000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
38	chr7:150437400-150443200	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
39	chr7:150437600-150438000	Weak transcription	Left Ventricle	heart
40	chr7:150437600-150438000	Weak transcription	Lung	lung
41	chr7:150437600-150438000	Weak transcription	Spleen	Spleen
42	chr7:150437600-150438600	Weak transcription	Right Ventricle	heart
43	chr7:150437600-150438800	Weak transcription	Fetal Muscle Leg	muscle
44	chr7:150437600-150439000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr7:150437600-150439000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr7:150437600-150439400	Weak transcription	Fetal Stomach	stomach
47	chr7:150437600-150439400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr7:150437600-150439600	Weak transcription	Esophagus	oesophagus
49	chr7:150437600-150439800	Weak transcription	Brain Hippocampus Middle	brain
50	chr7:150437600-150443200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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