Variant report

Variant	rs2441979
Chromosome Location	chr11:57831373-57831374
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57594227..57596364-chr11:57829897..57831561,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1013447	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10750876	0.86[GIH][hapmap]
rs10750878	0.98[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs10750882	0.91[GIH][hapmap]
rs10792127	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10792130	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10896696	0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs11229236	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229237	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1123196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1123306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1123307	0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs12363350	0.91[GIH][hapmap]
rs1374570	0.82[JPT][hapmap]
rs1447169	0.91[GIH][hapmap]
rs1545459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562863	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868043	0.98[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs2003375	0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs2100110	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2167357	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167358	0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs2218598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2441950	0.91[JPT][hapmap]
rs2441960	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2441961	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2441972	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2441977	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2443445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2443449	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2443450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2513705	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2513713	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2513726	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2513727	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2513728	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2513729	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2513730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2514181	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2514186	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2514187	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2514191	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2514199	0.99[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2514202	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2866830	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs3974323	0.91[GIH][hapmap]
rs4939176	0.98[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4939182	0.91[GIH][hapmap]
rs6591455	0.91[GIH][hapmap]
rs7111942	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7117711	0.91[GIH][hapmap]
rs7118536	0.98[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs7119421	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs896300	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs921132	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs921133	0.84[CEU][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap]
rs921134	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs921135	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs971066	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976429	0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs976430	0.81[AMR][1000 genomes];0.82[EUR][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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv832165	chr11:57806024-58009076	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2441979	MS4A8B	cis	cerebellum	SCAN
rs2441979	OR4C6	cis	parietal	SCAN
rs2441979	MS4A6A	cis	parietal	SCAN
rs2441979	OR8J3	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57826400-57838000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:57826400-57845200	Weak transcription	Pancreas	Pancrea
3	chr11:57828600-57835200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:57829400-57833400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:57830000-57831600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr11:57830000-57831800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr11:57830000-57831800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr11:57830000-57835000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:57830000-57836400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:57830200-57831400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:57830200-57831400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:57830400-57831800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:57830400-57832400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:57830600-57832000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:57830600-57834200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:57830600-57835000	Weak transcription	NHEK	skin
17	chr11:57831200-57834400	Enhancers	HepG2	liver

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