Variant report

Variant	rs6953522
Chromosome Location	chr7:112565546-112565547
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	chr7:112554744..112557418-chr7:112564931..112568212,3	MCF-7	breast:
2	chr7:112565275..112568159-chr7:112573101..112575582,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10237980	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10246678	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10249952	1.00[CHB][hapmap]
rs10261874	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10273589	0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10275208	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs11762737	0.83[CHD][hapmap]
rs11768787	0.82[CHD][hapmap]
rs1227163	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1227171	0.84[ASW][hapmap];0.95[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap]
rs1227174	0.85[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap]
rs1227181	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1227190	0.85[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap]
rs1238698	0.85[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap]
rs12535487	0.91[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12539085	0.92[ASW][hapmap];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];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1530756	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs1533851	0.85[EUR][1000 genomes]
rs1547554	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs17160078	1.00[CHB][hapmap]
rs1718944	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1718948	0.83[EUR][1000 genomes]
rs1718961	0.85[EUR][1000 genomes]
rs1718967	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs17405723	0.83[CHD][hapmap]
rs1796492	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap]
rs1796493	0.85[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap]
rs1796512	0.83[EUR][1000 genomes]
rs1796516	0.85[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap]
rs1996843	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2396573	0.86[EUR][1000 genomes]
rs2396574	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2457	0.85[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap]
rs2687267	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2708295	0.83[EUR][1000 genomes]
rs2708296	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs35548417	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3997335	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs3997336	0.86[EUR][1000 genomes]
rs494324	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs548994	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549688	0.85[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552304	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs564494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs565641	0.81[EUR][1000 genomes]
rs62472532	0.85[EUR][1000 genomes]
rs6466421	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs660743	0.85[JPT][hapmap]
rs672911	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs685259	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6944843	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs6948575	0.93[GIH][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs6967716	0.84[EUR][1000 genomes]
rs7777973	0.85[ASW][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs7781871	1.00[CHB][hapmap]
rs7785774	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7803405	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7806781	0.82[CHB][hapmap]
rs7808616	1.00[CHB][hapmap]
rs821782	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs821783	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs821785	0.85[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs821787	0.85[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9969347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	esv1794529	chr7:112400060-112588376	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2754368	chr7:112483049-112588049	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2758131	chr7:112492127-112768628	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2759556	chr7:112492127-112768628	Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6953522	CAV2	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112522200-112571000	Weak transcription	Thymus	Thymus
2	chr7:112530400-112576600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr7:112538800-112565600	Weak transcription	Pancreas	Pancrea
4	chr7:112541400-112578800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:112546400-112566000	Weak transcription	Right Ventricle	heart
6	chr7:112549200-112569000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:112549200-112571000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr7:112549400-112574200	Weak transcription	Fetal Brain Female	brain
9	chr7:112549600-112565800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:112551400-112566200	Weak transcription	Aorta	Aorta
11	chr7:112551600-112565800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr7:112551600-112571000	Weak transcription	HSMM	muscle
13	chr7:112551600-112575600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr7:112551600-112575800	Weak transcription	GM12878-XiMat	blood
15	chr7:112551600-112576200	Weak transcription	Ovary	ovary
16	chr7:112551600-112577400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:112551600-112578600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr7:112551600-112579400	Weak transcription	Spleen	Spleen
19	chr7:112553800-112578800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:112554000-112566000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:112554000-112570200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:112554000-112577200	Weak transcription	Primary B cells from cord blood	blood
23	chr7:112554200-112569600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr7:112555400-112570200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:112555400-112570600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr7:112555400-112578000	Weak transcription	Adipose Nuclei	Adipose
27	chr7:112555600-112569800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:112555600-112571000	Weak transcription	Dnd41	blood
29	chr7:112555600-112572600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr7:112555800-112567600	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr7:112556000-112573600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr7:112556200-112575800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr7:112556600-112571000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr7:112556800-112566000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:112556800-112570400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr7:112556800-112570800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:112556800-112571000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr7:112556800-112573000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:112556800-112576200	Weak transcription	Left Ventricle	heart
40	chr7:112556800-112577600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr7:112557000-112578600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr7:112562200-112572600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr7:112562800-112576400	Weak transcription	Fetal Intestine Small	intestine
44	chr7:112563200-112571000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr7:112563200-112578200	Weak transcription	HUVEC	blood vessel
46	chr7:112563600-112571000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr7:112565000-112566800	Enhancers	Fetal Heart	heart
48	chr7:112565200-112578600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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