Variant report

Variant	rs12544236
Chromosome Location	chr8:92139254-92139255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr8:92139060-92140427	SK-N-SH	brain:	n/a	chr8:92140353-92140361 chr8:92139785-92139799

Variant related genes	Relation type
LRRC69	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10100069	0.82[EUR][1000 genomes]
rs10111323	0.93[EUR][1000 genomes]
rs10956794	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11777826	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11778758	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11783034	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11785003	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12540975	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12546650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12677214	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28372564	0.85[EUR][1000 genomes]
rs34520902	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34548877	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35066004	0.92[EUR][1000 genomes]
rs35606777	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3885968	0.93[EUR][1000 genomes]
rs3885969	0.93[EUR][1000 genomes]
rs4129720	0.89[EUR][1000 genomes]
rs4259383	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4524748	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4577919	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4620242	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5029071	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55762572	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55779688	0.81[AMR][1000 genomes]
rs56004977	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56084507	0.85[ASN][1000 genomes]
rs56306245	0.82[EUR][1000 genomes]
rs57771593	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61279214	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62526680	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62526682	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62526683	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62526685	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62526686	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62526707	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62526730	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62531560	0.88[ASN][1000 genomes]
rs6471268	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6987417	0.85[AMR][1000 genomes]
rs6987764	0.85[AMR][1000 genomes]
rs7813523	0.80[AMR][1000 genomes]
rs7841266	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028628	chr8:91680968-92418954	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv539672	chr8:91680968-92418954	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv2758623	chr8:91974499-92273724	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2759629	chr8:91974499-92273724	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv831390	chr8:92037011-92198605	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv611721	chr8:92107070-92183658	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv891186	chr8:92110936-92187738	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv891187	chr8:92110936-92188940	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv891188	chr8:92110936-92191011	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv533559	chr8:92116009-92175700	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1027865	chr8:92118995-92179965	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1024251	chr8:92118995-92186057	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv525292	chr8:92123208-92174115	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv465736	chr8:92123208-92174115	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv611722	chr8:92123208-92174115	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv611723	chr8:92123208-92183658	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv891189	chr8:92123208-92188940	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv1028288	chr8:92124763-92186057	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	esv2757282	chr8:92127463-92183838	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	esv35058	chr8:92127463-92218776	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12544236	SLC26A7	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:92083000-92147800	Weak transcription	Spleen	Spleen
2	chr8:92083600-92150800	Weak transcription	Pancreas	Pancrea
3	chr8:92092600-92147800	Weak transcription	Right Ventricle	heart
4	chr8:92097400-92146200	Weak transcription	Psoas Muscle	Psoas
5	chr8:92104800-92148000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr8:92107200-92141000	Weak transcription	HMEC	breast
7	chr8:92109200-92147600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr8:92111600-92140800	Weak transcription	Brain Substantia Nigra	brain
9	chr8:92115400-92147800	Weak transcription	Esophagus	oesophagus
10	chr8:92117200-92140000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr8:92120400-92146800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr8:92121400-92148200	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr8:92121800-92152800	Weak transcription	NHEK	skin
14	chr8:92121800-92153600	Weak transcription	Liver	Liver
15	chr8:92124600-92154800	Weak transcription	Gastric	stomach
16	chr8:92124800-92140200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr8:92124800-92154800	Weak transcription	Lung	lung
18	chr8:92125000-92146400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr8:92125000-92156400	Weak transcription	Adipose Nuclei	Adipose
20	chr8:92125600-92146200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr8:92125600-92150200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr8:92125800-92143600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr8:92125800-92145800	Weak transcription	HSMM	muscle
24	chr8:92126600-92150400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr8:92127000-92145400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr8:92130800-92147200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr8:92131400-92149200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr8:92133000-92149000	Weak transcription	Aorta	Aorta
29	chr8:92135800-92149200	Weak transcription	Primary B cells from cord blood	blood
30	chr8:92137400-92139400	Strong transcription	GM12878-XiMat	blood
31	chr8:92137400-92140200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr8:92137600-92142200	Enhancers	Colon Smooth Muscle	Colon
33	chr8:92137600-92145400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr8:92137800-92142200	Enhancers	Rectal Smooth Muscle	rectum
35	chr8:92138200-92139600	Strong transcription	Left Ventricle	heart
36	chr8:92139000-92139800	Strong transcription	Primary T cells from cord blood	blood
37	chr8:92139000-92140000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr8:92139000-92140000	Enhancers	Stomach Smooth Muscle	stomach
39	chr8:92139200-92139600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr8:92139200-92139800	Enhancers	Fetal Stomach	stomach
41	chr8:92139200-92140400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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