Variant report

Variant	rs12641022
Chromosome Location	chr4:48866742-48866743
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	chr4:48853189..48856829-chr4:48863048..48867064,3	K562	blood:

Variant related genes	Relation type
ENSG00000109180	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11727343	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11729065	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11733534	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11734191	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11939889	0.83[EUR][1000 genomes]
rs11943219	0.83[EUR][1000 genomes]
rs12374247	0.83[ASN][1000 genomes]
rs12512637	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13109500	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13119414	0.84[EUR][1000 genomes]
rs13141838	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13149083	0.84[ASN][1000 genomes]
rs13152270	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1463365	0.85[ASN][1000 genomes]
rs1980193	0.84[EUR][1000 genomes]
rs2176460	0.84[EUR][1000 genomes]
rs2289065	0.83[ASN][1000 genomes]
rs2572345	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2572350	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2712156	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2712157	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2712158	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2712159	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2883562	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34730980	0.84[ASN][1000 genomes]
rs3761729	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4694904	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4694906	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4695400	0.83[EUR][1000 genomes]
rs4695401	0.83[EUR][1000 genomes]
rs4695407	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57797824	0.84[EUR][1000 genomes]
rs62310934	0.90[ASN][1000 genomes]
rs6447655	0.81[EUR][1000 genomes]
rs6830078	0.83[EUR][1000 genomes]
rs7654032	0.84[ASN][1000 genomes]
rs7657332	0.84[EUR][1000 genomes]
rs7657698	0.83[EUR][1000 genomes]
rs7665209	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7680280	0.81[EUR][1000 genomes]
rs7681070	0.81[EUR][1000 genomes]
rs7685360	0.82[ASN][1000 genomes]
rs7687992	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7697522	0.82[EUR][1000 genomes]
rs9291326	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9637562	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9790336	0.81[EUR][1000 genomes]
rs9997920	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12641022	OCIAD1	cis	Esophagus Muscularis	GTEx
rs12641022	SLC10A4	cis	lung	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48838200-48866800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:48848200-48880000	Weak transcription	Brain Substantia Nigra	brain
3	chr4:48860400-48882200	Weak transcription	Gastric	stomach
4	chr4:48860400-48901400	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:48860600-48868600	Weak transcription	Fetal Kidney	kidney
6	chr4:48860600-48872600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:48860600-48873600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:48860800-48871800	Weak transcription	Ovary	ovary
9	chr4:48860800-48871800	Weak transcription	Pancreas	Pancrea
10	chr4:48860800-48872000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:48860800-48872400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:48860800-48873000	Weak transcription	Primary T cells from cord blood	blood
13	chr4:48860800-48892000	Weak transcription	Thymus	Thymus
14	chr4:48860800-48892800	Weak transcription	Aorta	Aorta
15	chr4:48860800-48892800	Weak transcription	Left Ventricle	heart
16	chr4:48860800-48895000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:48860800-48895000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:48863200-48867600	Weak transcription	Brain Anterior Caudate	brain
19	chr4:48863200-48871600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:48863600-48871800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:48863600-48892000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr4:48864200-48872600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links