Variant report

Variant	rs16956599
Chromosome Location	chr15:72447013-72447014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72445875..72448342-chr15:72461656..72463455,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175318	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11072341	0.88[ASN][1000 genomes]
rs11072343	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072344	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11072355	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs1120002	0.88[ASN][1000 genomes]
rs12438532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12439689	0.92[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];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12440299	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[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];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12441470	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12441567	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12441622	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12442680	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12443127	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12592615	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12592932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12592969	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[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];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12593857	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12593946	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12594297	0.90[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	0.84[ASN][1000 genomes]
rs16953770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16956539	0.81[EUR][1000 genomes];0.88[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];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16956723	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
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];0.81[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];0.98[ASN][1000 genomes]
rs28397923	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28639924	0.88[ASN][1000 genomes]
rs28653163	0.88[ASN][1000 genomes]
rs28701834	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2912226	1.00[CEU][hapmap]
rs2912229	1.00[CEU][hapmap]
rs2929521	0.84[ASN][1000 genomes]
rs2929522	0.84[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];0.82[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];0.81[ASN][1000 genomes]
rs2957369	0.84[ASN][1000 genomes]
rs2957741	0.84[ASN][1000 genomes]
rs2957747	0.84[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];0.86[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];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35773391	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[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];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3825869	0.84[ASN][1000 genomes]
rs4442765	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4511484	0.84[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	0.81[EUR][1000 genomes];0.88[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];0.90[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];0.96[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];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7177067	0.83[AFR][1000 genomes]
rs7178613	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]
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];1.00[EUR][1000 genomes];0.81[ASN][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];1.00[EUR][1000 genomes];0.94[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];0.88[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];0.81[EUR][1000 genomes];0.94[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	0.88[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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72428400-72447400	Weak transcription	Pancreas	Pancrea
2	chr15:72430000-72447200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:72430600-72447400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:72431400-72447600	Weak transcription	Spleen	Spleen
5	chr15:72434400-72447400	Weak transcription	HSMM	muscle
6	chr15:72440200-72447400	Weak transcription	Brain Angular Gyrus	brain
7	chr15:72440200-72447600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:72440400-72447400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr15:72445200-72447400	Enhancers	Stomach Smooth Muscle	stomach
10	chr15:72445600-72447400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr15:72445800-72447200	Enhancers	Fetal Heart	heart
12	chr15:72445800-72447200	Enhancers	A549	lung
13	chr15:72445800-72447400	Enhancers	Fetal Kidney	kidney
14	chr15:72445800-72447400	Enhancers	Stomach Mucosa	stomach
15	chr15:72445800-72448000	Enhancers	Fetal Lung	lung
16	chr15:72446000-72447400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:72446200-72447200	Weak transcription	Brain Substantia Nigra	brain
18	chr15:72446200-72447200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:72446200-72447200	Weak transcription	Fetal Brain Female	brain
20	chr15:72446200-72447400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:72446200-72447400	Weak transcription	Aorta	Aorta
22	chr15:72446200-72447400	Weak transcription	Brain Germinal Matrix	brain
23	chr15:72446200-72447400	Weak transcription	Brain Hippocampus Middle	brain
24	chr15:72446200-72447400	Weak transcription	Colon Smooth Muscle	Colon
25	chr15:72446200-72447400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr15:72446200-72447400	Weak transcription	NHLF	lung
27	chr15:72446400-72447400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:72446400-72447400	Weak transcription	Fetal Stomach	stomach
29	chr15:72446400-72447800	Enhancers	Lung	lung
30	chr15:72446400-72448200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:72446600-72447400	Enhancers	HMEC	breast
32	chr15:72446600-72447600	Enhancers	Fetal Muscle Leg	muscle
33	chr15:72446600-72447800	Enhancers	Fetal Brain Male	brain
34	chr15:72446800-72447200	Weak transcription	Brain Anterior Caudate	brain
35	chr15:72446800-72447200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:72446800-72447200	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr15:72446800-72447200	Weak transcription	HUVEC	blood vessel
38	chr15:72446800-72447400	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr15:72446800-72447400	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr15:72447000-72447400	Enhancers	Liver	Liver
41	chr15:72447000-72447400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr15:72447000-72447600	Weak transcription	Gastric	stomach
43	chr15:72447000-72447800	Weak transcription	Primary monocytes fromperipheralblood	blood

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