Variant report

Variant	rs10499952
Chromosome Location	chr7:102567747-102567748
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	chr7:102562952..102565366-chr7:102565830..102568184,3	MCF-7	breast:
2	chr7:102558852..102560445-chr7:102565710..102568123,2	K562	blood:

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10257543	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10267275	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs10273725	0.92[CEU][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10435335	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10487283	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs1100044	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11543736	0.93[EUR][1000 genomes]
rs11970869	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11972019	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11972644	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11973870	0.94[EUR][1000 genomes]
rs11978670	0.91[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11978768	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs11978799	0.92[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11980643	0.90[EUR][1000 genomes]
rs11981980	0.85[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs11983456	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs11983521	0.82[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs12056296	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12532495	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12533386	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12538955	0.80[EUR][1000 genomes]
rs12540384	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12666764	0.84[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs12667218	0.94[EUR][1000 genomes]
rs12668434	0.85[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs12669668	0.82[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs12671803	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13242493	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs17136090	0.85[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs17136137	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2009503	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2159022	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2190673	0.99[EUR][1000 genomes]
rs2228686	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2411056	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2411059	0.97[EUR][1000 genomes]
rs2908412	0.85[CEU][hapmap]
rs35479298	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3779029	0.94[EUR][1000 genomes]
rs41501847	0.92[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4296965	0.95[EUR][1000 genomes]
rs4400322	0.84[AFR][1000 genomes]
rs56894117	0.94[EUR][1000 genomes]
rs56921864	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57350619	0.94[EUR][1000 genomes]
rs57368671	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57545514	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57616389	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57776797	0.94[EUR][1000 genomes]
rs58191643	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58680618	0.88[EUR][1000 genomes]
rs58814323	0.82[EUR][1000 genomes]
rs58919995	0.80[EUR][1000 genomes]
rs59278165	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59544295	0.81[EUR][1000 genomes]
rs59709436	0.81[EUR][1000 genomes]
rs60524601	0.94[EUR][1000 genomes]
rs60599650	0.94[EUR][1000 genomes]
rs61404409	0.84[AFR][1000 genomes]
rs61679881	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6465877	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6465878	0.85[CEU][hapmap];0.96[EUR][1000 genomes]
rs6465879	0.91[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6465882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6465885	0.91[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6942855	0.91[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6945369	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs6946773	0.82[ASW][hapmap];0.85[CEU][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap]
rs6947403	1.00[CEU][hapmap];0.98[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6949150	0.92[CEU][hapmap];0.85[CHB][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6951288	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs6953980	0.92[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6956781	0.91[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6957434	0.91[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6957771	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6967389	0.82[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs6968713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6973081	0.82[ASW][hapmap];0.81[LWK][hapmap];0.92[MKK][hapmap];0.81[AFR][1000 genomes]
rs6975451	0.91[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6976005	0.94[EUR][1000 genomes]
rs6977145	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73406284	0.97[EUR][1000 genomes]
rs73406302	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73408204	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73408241	0.85[AFR][1000 genomes]
rs73408250	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7779145	0.85[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7779618	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7780405	0.92[CEU][hapmap];0.88[GIH][hapmap]
rs7780981	0.85[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs7796335	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7800387	0.84[CEU][hapmap]
rs7804322	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs847646	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs847647	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs847652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs847656	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs847658	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs865865	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs955992	0.92[CEU][hapmap]
rs9690210	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS 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 miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv608058	chr7:102466741-102571713	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv464667	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv608060	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats 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	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10499952	LRWD1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102517200-102578200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:102565200-102569200	Enhancers	Fetal Lung	lung
3	chr7:102565800-102569800	Genic enhancers	HSMM	muscle
4	chr7:102566000-102567800	Enhancers	NHLF	lung
5	chr7:102566000-102568000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr7:102566000-102568400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr7:102566200-102568800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:102566400-102567800	Enhancers	NHDF-Ad	bronchial
9	chr7:102566400-102568200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:102566400-102568200	Genic enhancers	K562	blood
11	chr7:102566400-102568200	Enhancers	NH-A	brain
12	chr7:102566400-102568400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr7:102566400-102568600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr7:102566400-102568600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr7:102566400-102568600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr7:102566400-102568600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:102566400-102568600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:102566400-102568600	Enhancers	Osteobl	bone
19	chr7:102566600-102568200	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr7:102566600-102568200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:102566600-102568200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:102566600-102568400	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr7:102566600-102568400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr7:102566600-102568400	Enhancers	Hela-S3	cervix
25	chr7:102566600-102568600	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr7:102566600-102568600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr7:102566600-102568600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr7:102566600-102568600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr7:102566600-102568600	Enhancers	A549	lung
30	chr7:102566600-102568800	Enhancers	Brain Germinal Matrix	brain
31	chr7:102566600-102569400	Weak transcription	Psoas Muscle	Psoas
32	chr7:102566800-102567800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr7:102566800-102568000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:102566800-102568000	Weak transcription	Aorta	Aorta
35	chr7:102566800-102568000	Weak transcription	Ovary	ovary
36	chr7:102566800-102568000	Weak transcription	Right Atrium	heart
37	chr7:102566800-102568200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr7:102566800-102568800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr7:102566800-102573000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr7:102567000-102568200	Enhancers	HMEC	breast
41	chr7:102567200-102573200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr7:102567400-102567800	Weak transcription	Fetal Kidney	kidney
43	chr7:102567400-102568000	Enhancers	Fetal Stomach	stomach
44	chr7:102567400-102568200	Enhancers	NHEK	skin
45	chr7:102567600-102567800	Flanking Active TSS	HSMMtube	muscle
46	chr7:102567600-102568600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr7:102567600-102568600	Enhancers	Placenta Amnion	Placenta Amnion
48	chr7:102567600-102573000	Weak transcription	Fetal Muscle Leg	muscle
49	chr7:102567600-102573600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:102567600-102574000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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