Variant report

Variant	rs12419334
Chromosome Location	chr11:71139472-71139473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:71138540..71142714-chr11:71144455..71147360,4	K562	blood:
2	chr11:71137647..71140040-chr11:71141812..71145984,4	K562	blood:
3	chr11:71139168..71142453-chr11:71148977..71152491,3	K562	blood:
4	chr11:71137158..71140424-chr11:71155885..71157748,3	K562	blood:
5	chr11:71138911..71140880-chr11:71154532..71157322,2	K562	blood:

Variant related genes	Relation type
ENSG00000172893	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1044482	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11233746	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11233747	0.95[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11233789	0.81[EUR][1000 genomes]
rs11546509	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11600569	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11600860	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11603330	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11604642	0.85[ASN][1000 genomes]
rs11606033	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11606612	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11606631	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12278461	0.81[EUR][1000 genomes]
rs12419279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422045	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12785878	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12789253	0.80[ASN][1000 genomes]
rs12789751	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12790010	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12790558	0.94[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12791871	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12792306	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12793224	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12793530	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12793607	0.80[ASN][1000 genomes]
rs12794668	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12797951	0.87[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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12800438	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12803256	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12806844	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12806918	0.81[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap]
rs12807718	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12807827	0.81[ASN][1000 genomes]
rs12808368	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1630498	0.84[TSI][hapmap]
rs1790324	0.84[TSI][hapmap]
rs1790345	0.84[TSI][hapmap]
rs1792229	0.80[TSI][hapmap]
rs1792280	0.81[EUR][1000 genomes]
rs1792282	0.84[TSI][hapmap]
rs1792284	0.84[TSI][hapmap]
rs1981412	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2002063	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2002064	0.80[TSI][hapmap]
rs2040323	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2276360	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2276361	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2276362	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2282620	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs2282621	0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs28364617	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2852853	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3750997	1.00[CEU][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3763856	0.80[ASN][1000 genomes]
rs3794060	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4423214	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4488226	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4944044	0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs4944062	0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944946	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4944949	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4944955	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4944956	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4944957	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[TSI][hapmap]
rs4944958	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4944959	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4944996	0.81[ASN][1000 genomes]
rs4945008	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs732934	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs736894	0.84[TSI][hapmap]
rs7928249	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7935125	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7938885	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7944926	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs909217	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12419334	RP11-660L16.2	cis	Thyroid	GTEx
rs12419334	RP11-660L16.2	cis	Whole Blood	GTEx
rs12419334	NADSYN1	cis	Thyroid	GTEx
rs12419334	NADSYN1	cis	Nerve Tibial	GTEx
rs12419334	FOLR3	cis	parietal	SCAN
rs12419334	RP11-660L16.2	cis	Nerve Tibial	GTEx
rs12419334	RP11-660L16.2	cis	Adipose Subcutaneous	GTEx
rs12419334	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs12419334	DHCR7	cis	cerebellum	SCAN
rs12419334	RAB6A	cis	cerebellum	SCAN
rs12419334	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12419334	RP11-660L16.2	cis	Esophagus Muscularis	GTEx
rs12419334	RP11-660L16.2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71123600-71139600	Weak transcription	Right Atrium	heart
2	chr11:71132600-71144000	Weak transcription	Spleen	Spleen
3	chr11:71135000-71150600	Weak transcription	NH-A	brain
4	chr11:71135400-71139600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr11:71135400-71145000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:71137000-71140000	Weak transcription	Stomach Mucosa	stomach
7	chr11:71137000-71144800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:71137200-71140200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:71137200-71144000	Weak transcription	Hela-S3	cervix
10	chr11:71137200-71145000	Weak transcription	Brain Germinal Matrix	brain
11	chr11:71137200-71149600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr11:71137600-71146000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr11:71137800-71139600	Weak transcription	Adipose Nuclei	Adipose
14	chr11:71137800-71140000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:71138000-71144800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:71138000-71145200	Weak transcription	HMEC	breast
17	chr11:71139200-71145000	Weak transcription	GM12878-XiMat	blood
18	chr11:71139200-71145800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:71139400-71140200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:71139400-71141000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr11:71139400-71145000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links