Variant report

Variant	rs6495057
Chromosome Location	chr15:73421239-73421240
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	chr15:73421059..73423677-chr15:73433807..73436410,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259691	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1017808	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10518997	1.00[YRI][hapmap]
rs11072405	0.90[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs11072407	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11072408	0.85[ASN][1000 genomes]
rs11072411	1.00[ASW][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap]
rs1119251	0.86[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11634045	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11636981	1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11856537	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12442755	0.89[ASW][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap]
rs12594776	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12595434	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12901272	0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs12901649	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs12912737	0.87[ASN][1000 genomes]
rs1382782	0.82[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1564347	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1585766	0.86[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs16957683	0.85[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1878940	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs1904335	0.88[ASN][1000 genomes]
rs2061890	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2252725	0.86[CHD][hapmap]
rs2292915	0.81[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap]
rs2415142	0.90[ASN][1000 genomes]
rs2415145	0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2415146	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2660821	0.95[CHD][hapmap];0.88[GIH][hapmap]
rs28742992	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34953385	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs35348961	0.85[ASN][1000 genomes]
rs35391014	0.84[ASN][1000 genomes]
rs35608416	0.84[ASN][1000 genomes]
rs36072085	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3743496	0.89[ASW][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs3784795	0.89[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs4776623	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4777585	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4777587	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4777588	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4777592	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs486267	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs489531	0.86[CHD][hapmap];0.82[GIH][hapmap]
rs498005	0.85[CHD][hapmap]
rs576813	0.81[CHB][hapmap]
rs59628124	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6495045	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6495046	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495050	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6495051	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495052	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6495053	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495058	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7163543	0.91[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs7168555	0.86[CEU][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7173710	0.83[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7177758	0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7184025	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7495084	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8032762	1.00[YRI][hapmap]
rs8039418	0.81[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs9806269	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs983067	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv482421	chr15:73279141-73426897	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv904339	chr15:73375847-73483718	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv904340	chr15:73375847-73524629	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904341	chr15:73390790-73483718	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv904342	chr15:73390790-73524629	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv527236	chr15:73421239-73469535	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6495057	CYP11A1	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73388800-73431200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:73393200-73422400	Weak transcription	Aorta	Aorta
3	chr15:73396400-73444600	Weak transcription	Psoas Muscle	Psoas
4	chr15:73400400-73434200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:73401200-73423000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:73401200-73428200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:73401400-73422400	Weak transcription	Pancreas	Pancrea
8	chr15:73401400-73422800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:73401400-73480200	Weak transcription	Right Ventricle	heart
10	chr15:73403000-73443400	Weak transcription	Fetal Kidney	kidney
11	chr15:73404200-73425800	Weak transcription	Small Intestine	intestine
12	chr15:73404200-73442600	Weak transcription	Left Ventricle	heart
13	chr15:73406600-73422400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:73406600-73423200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:73406600-73425200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:73406600-73432600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr15:73407400-73431600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:73408000-73443400	Weak transcription	Adipose Nuclei	Adipose
19	chr15:73408800-73424600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:73409200-73422800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:73409200-73429200	Weak transcription	Esophagus	oesophagus
22	chr15:73410600-73434600	Weak transcription	Liver	Liver
23	chr15:73410800-73431400	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:73413200-73437200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:73413400-73434200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:73413600-73446400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr15:73414000-73428200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:73414000-73437000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:73414000-73440000	Weak transcription	Fetal Brain Female	brain
30	chr15:73414200-73428600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr15:73414200-73445600	Weak transcription	Brain Substantia Nigra	brain
32	chr15:73414400-73458200	Weak transcription	Colonic Mucosa	Colon
33	chr15:73414600-73436600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:73414800-73421800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr15:73415000-73425400	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr15:73415200-73422800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr15:73415400-73423800	Weak transcription	Fetal Heart	heart
38	chr15:73415400-73446600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:73415600-73428400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:73416000-73453200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr15:73416600-73422200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr15:73416600-73428400	Weak transcription	Fetal Lung	lung
43	chr15:73416600-73444600	Weak transcription	Fetal Muscle Leg	muscle
44	chr15:73416600-73444600	Weak transcription	Lung	lung
45	chr15:73416800-73422600	Weak transcription	Fetal Stomach	stomach
46	chr15:73416800-73448800	Weak transcription	Ovary	ovary
47	chr15:73417000-73443000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr15:73417400-73423200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr15:73418200-73433200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr15:73418600-73430600	Weak transcription	Fetal Brain Male	brain

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