Variant report

Variant	rs2159022
Chromosome Location	chr7:102513998-102513999
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	chr7:102513883..102516664-chr7:102520756..102522395,2	K562	blood:

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10257543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10267275	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10273725	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs10435335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10487283	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10499952	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]
rs1100044	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11543736	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11970869	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11972019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11972644	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11973870	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11978670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11978768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11978799	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs11980643	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11981980	0.92[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap]
rs11983456	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11983521	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12056296	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532495	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12533386	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12538955	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12540384	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12666764	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12667218	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12668434	0.92[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs12669668	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12671803	0.93[EUR][1000 genomes]
rs13242493	0.92[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17136090	0.92[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs17136137	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2009503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2190673	0.96[EUR][1000 genomes]
rs2228686	0.83[EUR][1000 genomes]
rs2411056	0.96[EUR][1000 genomes]
rs2411059	0.94[EUR][1000 genomes]
rs2908412	0.92[CEU][hapmap]
rs35479298	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3779029	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41501847	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs4296965	0.92[EUR][1000 genomes]
rs56894117	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56921864	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57253646	0.80[EUR][1000 genomes]
rs57350619	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57368671	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57545514	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57616389	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57776797	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58191643	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58680618	0.92[EUR][1000 genomes]
rs58814323	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58919995	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59278165	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59544295	0.82[EUR][1000 genomes]
rs59709436	0.82[EUR][1000 genomes]
rs60524601	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60599650	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61679881	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6465877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6465878	0.92[CEU][hapmap];0.82[YRI][hapmap];0.99[EUR][1000 genomes]
rs6465879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6465882	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6465885	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6942855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6945369	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6946773	0.92[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs6947403	1.00[ASW][hapmap];0.92[CEU][hapmap];0.86[GIH][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[EUR][1000 genomes]
rs6949150	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6951288	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6953980	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs6956781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6957434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6957771	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6967389	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6968713	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6975388	0.80[EUR][1000 genomes]
rs6975451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6976005	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6977145	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73406250	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73406284	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73406302	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73408204	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73408250	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7779145	0.92[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs7779618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7780405	0.84[CEU][hapmap]
rs7780981	0.92[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs7796335	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7800387	0.91[CEU][hapmap]
rs7804322	0.96[EUR][1000 genomes]
rs847646	0.96[EUR][1000 genomes]
rs847647	0.92[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap]
rs847652	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs847656	0.81[ASW][hapmap];0.92[CEU][hapmap];0.88[GIH][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.96[EUR][1000 genomes]
rs847658	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs865865	0.96[EUR][1000 genomes]
rs955992	0.84[CEU][hapmap]
rs9690210	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv470382	chr7:102375663-102538515	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv608057	chr7:102440184-102538515	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	nsv5880	chr7:102505158-102550471	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2159022	LRWD1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102470000-102516400	Weak transcription	Pancreas	Pancrea
2	chr7:102500600-102514200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr7:102500600-102518400	Weak transcription	Left Ventricle	heart
4	chr7:102501200-102515800	Weak transcription	Gastric	stomach
5	chr7:102501200-102530800	Weak transcription	Ovary	ovary
6	chr7:102502600-102516200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr7:102504800-102516200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:102507400-102519400	Weak transcription	Fetal Kidney	kidney
9	chr7:102508000-102522200	Weak transcription	Fetal Stomach	stomach
10	chr7:102508000-102529200	Weak transcription	Fetal Lung	lung
11	chr7:102508600-102514800	Strong transcription	K562	blood
12	chr7:102512200-102514200	Enhancers	HSMM	muscle
13	chr7:102512200-102517000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:102512200-102517400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr7:102512200-102517400	Enhancers	Hela-S3	cervix
16	chr7:102512200-102517600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:102512200-102517600	Enhancers	HMEC	breast
18	chr7:102512200-102517600	Enhancers	NHDF-Ad	bronchial
19	chr7:102512400-102514000	Enhancers	HepG2	liver
20	chr7:102512400-102514200	Enhancers	A549	lung
21	chr7:102512400-102516600	Enhancers	HSMMtube	muscle
22	chr7:102512400-102517200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr7:102512400-102517200	Enhancers	NHLF	lung
24	chr7:102512400-102517400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr7:102512400-102517400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr7:102512600-102514000	Weak transcription	Fetal Muscle Leg	muscle
27	chr7:102512600-102517400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr7:102512600-102517600	Enhancers	NHEK	skin
29	chr7:102512800-102517400	Enhancers	Osteobl	bone
30	chr7:102512800-102517600	Enhancers	NH-A	brain
31	chr7:102513000-102516800	Enhancers	Placenta Amnion	Placenta Amnion
32	chr7:102513000-102517800	Enhancers	HUVEC	blood vessel
33	chr7:102513400-102514000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:102513400-102514600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr7:102513400-102514800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr7:102513400-102517000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:102513400-102517000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr7:102513600-102514200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr7:102513800-102514000	ZNF genes & repeats	Aorta	Aorta
40	chr7:102513800-102516000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:102513800-102516800	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr7:102513800-102517200	Enhancers	Stomach Mucosa	stomach
43	chr7:102513800-102531600	Weak transcription	Fetal Brain Male	brain

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