Variant report

Variant	rs7178613
Chromosome Location	chr15:72428716-72428717
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	chr15:72409540..72412383-chr15:72425883..72429173,3	MCF-7	breast:
2	chr15:72425861..72427575-chr15:72427612..72429350,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243568	Chromatin interaction
ENSG00000066933	Chromatin interaction
ENSG00000166192	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11072341	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11072343	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072344	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072355	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs1120002	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12437582	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12438532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12439689	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12440204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12440299	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12440435	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12440927	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs12441246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12441470	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12441567	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12441622	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12442680	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12443127	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12592615	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12592858	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12592932	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12592969	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12593082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12593857	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12593946	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12594297	0.81[EUR][1000 genomes]
rs12911449	1.00[CEU][hapmap]
rs1426168	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1545825	0.87[ASN][1000 genomes]
rs16953770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16956539	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16956599	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];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16956602	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];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1871834	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];0.84[ASN][1000 genomes]
rs2288256	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs2305705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28397923	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28639924	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28653163	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28701834	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2912226	1.00[CEU][hapmap]
rs2912229	1.00[CEU][hapmap]
rs2929514	0.81[ASN][1000 genomes]
rs2929515	0.81[ASN][1000 genomes]
rs2929521	0.87[ASN][1000 genomes]
rs2929522	0.87[ASN][1000 genomes]
rs2929524	0.81[ASN][1000 genomes]
rs2929530	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];0.85[ASN][1000 genomes]
rs2929531	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2929533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2957369	0.87[ASN][1000 genomes]
rs2957729	0.81[ASN][1000 genomes]
rs2957730	0.81[ASN][1000 genomes]
rs2957733	0.81[ASN][1000 genomes]
rs2957741	0.87[ASN][1000 genomes]
rs2957747	0.87[ASN][1000 genomes]
rs2957749	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];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2959915	1.00[CEU][hapmap]
rs34625473	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];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35773391	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3803388	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3809505	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3825869	0.87[ASN][1000 genomes]
rs4511484	0.87[ASN][1000 genomes]
rs6495000	1.00[CEU][hapmap]
rs7161909	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7164646	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7165735	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7171446	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7175907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7177067	0.83[AFR][1000 genomes]
rs7178876	0.87[AFR][1000 genomes]
rs8026894	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs8029218	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8032957	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];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8039245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8192381	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9920148	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
6	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer 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	172 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72411400-72432000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr15:72411600-72433800	Weak transcription	Fetal Intestine Small	intestine
3	chr15:72412200-72431800	Weak transcription	Psoas Muscle	Psoas
4	chr15:72421000-72431400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:72421800-72433000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr15:72423800-72432000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr15:72424800-72432000	Weak transcription	GM12878-XiMat	blood
8	chr15:72426400-72432000	Weak transcription	Primary T cells from cord blood	blood
9	chr15:72426800-72436200	Weak transcription	Aorta	Aorta
10	chr15:72427000-72429200	Enhancers	A549	lung
11	chr15:72427400-72433800	Weak transcription	HepG2	liver
12	chr15:72427800-72428800	Enhancers	Fetal Kidney	kidney
13	chr15:72428000-72429800	Enhancers	Fetal Lung	lung
14	chr15:72428200-72428800	Enhancers	Fetal Stomach	stomach
15	chr15:72428200-72428800	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr15:72428200-72430000	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr15:72428400-72428800	Enhancers	Stomach Mucosa	stomach
18	chr15:72428400-72429800	Enhancers	Fetal Brain Female	brain
19	chr15:72428400-72431600	Weak transcription	Left Ventricle	heart
20	chr15:72428400-72431800	Weak transcription	Brain Anterior Caudate	brain
21	chr15:72428400-72433800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr15:72428400-72436000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:72428400-72440400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:72428400-72447400	Weak transcription	Pancreas	Pancrea
25	chr15:72428600-72428800	Enhancers	Small Intestine	intestine
26	chr15:72428600-72432000	Weak transcription	Brain Germinal Matrix	brain

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