Variant report

Variant	rs7168178
Chromosome Location	chr15:57012816-57012817
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	chr15:57010746..57014338-chr15:57023957..57026585,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1010700	0.84[EUR][1000 genomes]
rs10152127	0.80[AMR][1000 genomes]
rs10518870	0.84[CEU][hapmap]
rs11071287	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11630168	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes]
rs11632471	0.81[EUR][1000 genomes]
rs11633363	0.89[ASN][1000 genomes]
rs11635333	0.83[ASN][1000 genomes]
rs11636994	0.81[AMR][1000 genomes]
rs11638497	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638580	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11638707	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[ASN][1000 genomes]
rs11856558	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11857706	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12148500	0.81[AMR][1000 genomes]
rs12438709	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12442018	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12442189	0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs12591502	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs12592389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12593286	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12595822	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12898521	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12898760	0.89[ASN][1000 genomes]
rs12900244	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12900441	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12903283	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs12903336	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs12903862	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs12905514	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12906591	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12906830	0.83[ASN][1000 genomes]
rs12910459	0.85[CEU][hapmap]
rs12911381	0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs12912666	0.92[CEU][hapmap];0.85[CHB][hapmap];0.93[TSI][hapmap]
rs12913361	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12913871	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12913960	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1424694	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1477475	0.83[EUR][1000 genomes]
rs16977020	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs17238845	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap]
rs1895640	0.83[EUR][1000 genomes]
rs1979467	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs1994081	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2052640	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2161934	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2170459	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2170463	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs2279298	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2279299	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2414480	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28480089	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28575268	0.81[EUR][1000 genomes]
rs28620278	0.81[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap]
rs3784554	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3803457	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs3816752	0.84[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3929265	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4601984	0.90[EUR][1000 genomes]
rs4774244	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4774886	0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[ASN][1000 genomes]
rs521904	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs538382	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs553421	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs559736	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62022931	0.84[EUR][1000 genomes]
rs62022933	0.80[EUR][1000 genomes]
rs62022934	0.82[EUR][1000 genomes]
rs6493885	0.87[EUR][1000 genomes]
rs7162317	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7165831	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7169454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs795032	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8025391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8036217	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8041540	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8043223	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv569576	chr15:57012816-57126917	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56919800-57016600	Weak transcription	Small Intestine	intestine
2	chr15:56958400-57019200	Weak transcription	Fetal Intestine Small	intestine
3	chr15:56971000-57023400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:56992400-57021800	Weak transcription	Right Ventricle	heart
5	chr15:56992600-57022600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:56993000-57016000	Weak transcription	Pancreas	Pancrea
7	chr15:56993000-57024000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:56993400-57021600	Weak transcription	Fetal Brain Male	brain
9	chr15:56994000-57023800	Weak transcription	Fetal Kidney	kidney
10	chr15:56995800-57016000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:56995800-57022200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr15:56996000-57013000	Weak transcription	Ovary	ovary
13	chr15:56996000-57021800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:56996400-57015800	Weak transcription	Fetal Intestine Large	intestine
15	chr15:56996400-57021600	Weak transcription	HSMMtube	muscle
16	chr15:56996400-57022600	Weak transcription	NH-A	brain
17	chr15:56996800-57022600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:56997000-57016000	Weak transcription	HSMM	muscle
19	chr15:56997200-57015800	Weak transcription	Liver	Liver
20	chr15:56997200-57016400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:56997200-57016600	Weak transcription	Left Ventricle	heart
22	chr15:56997200-57022800	Weak transcription	Gastric	stomach
23	chr15:56997200-57023800	Weak transcription	Fetal Stomach	stomach
24	chr15:56998000-57016000	Weak transcription	Fetal Lung	lung
25	chr15:56998400-57013800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:56998400-57013800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:56998400-57016200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr15:56998400-57021200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:56998600-57015800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:56998800-57021800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:56998800-57023400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr15:56998800-57023800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr15:56999000-57013800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr15:56999200-57014000	Weak transcription	Fetal Muscle Leg	muscle
35	chr15:56999200-57017800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:56999400-57023400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:57008000-57017200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr15:57009200-57015800	Weak transcription	Stomach Mucosa	stomach
39	chr15:57009200-57021400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:57009400-57013000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr15:57009400-57015800	Weak transcription	Colon Smooth Muscle	Colon
42	chr15:57009400-57016000	Weak transcription	Brain Angular Gyrus	brain
43	chr15:57009400-57022800	Weak transcription	Right Atrium	heart
44	chr15:57009400-57024400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:57010400-57013600	Weak transcription	Brain Germinal Matrix	brain
46	chr15:57010800-57016000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr15:57011000-57022200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:57011200-57016400	Weak transcription	Brain Anterior Caudate	brain
49	chr15:57011200-57022600	Weak transcription	Fetal Heart	heart
50	chr15:57011400-57014400	Genic enhancers	Fetal Thymus	thymus

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