Variant report

Variant	rs2239131
Chromosome Location	chr12:2229059-2229060
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10848617	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1122864	0.84[CHB][hapmap]
rs1558321	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1558322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238027	0.80[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2238029	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2238031	0.82[AMR][1000 genomes]
rs2238033	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2238034	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs2238036	0.85[JPT][hapmap]
rs2239130	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2239133	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2239134	0.96[EUR][1000 genomes]
rs2239135	0.89[EUR][1000 genomes]
rs2247833	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs2283283	0.92[MEX][hapmap]
rs2299660	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2299661	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2299662	0.90[EUR][1000 genomes]
rs2299663	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2299664	1.00[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4126711	0.91[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4765897	0.89[EUR][1000 genomes]
rs4765898	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs6489348	0.82[GIH][hapmap];0.96[MEX][hapmap];0.80[AMR][1000 genomes]
rs6489349	0.80[AMR][1000 genomes]
rs7298821	0.81[GIH][hapmap];0.81[JPT][hapmap]
rs758723	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs874924	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs881303	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv521838	chr12:2060580-2299680	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1035885	chr12:2077660-2310157	Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv541350	chr12:2077660-2310157	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1038722	chr12:2085035-2308205	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv541351	chr12:2085035-2308205	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv826183	chr12:2147469-2257818	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv898603	chr12:2208390-2268143	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1053798	chr12:2214047-2253488	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv557033	chr12:2215448-2252924	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv1041740	chr12:2218997-2259643	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv557034	chr12:2226045-2251273	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1052890	chr12:2226045-2251869	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv557035	chr12:2227311-2252924	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv468967	chr12:2227311-2268143	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv557036	chr12:2227311-2268143	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2239131	KCNA1	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2217800-2229600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:2219000-2234000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:2220800-2235400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr12:2221800-2229600	Weak transcription	Fetal Brain Male	brain
5	chr12:2222000-2231200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:2222000-2235400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:2222400-2239000	Weak transcription	Brain Anterior Caudate	brain
8	chr12:2222800-2236000	Weak transcription	Lung	lung
9	chr12:2223200-2250200	Weak transcription	Brain Substantia Nigra	brain
10	chr12:2223400-2229600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:2223400-2234000	Weak transcription	Spleen	Spleen
12	chr12:2223600-2238200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:2224400-2231000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:2224600-2231200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:2225400-2233800	Weak transcription	Fetal Brain Female	brain
16	chr12:2226800-2231200	Enhancers	Rectal Smooth Muscle	rectum
17	chr12:2227200-2229600	Enhancers	Left Ventricle	heart
18	chr12:2227400-2231600	Enhancers	Fetal Lung	lung
19	chr12:2227600-2230600	Enhancers	Aorta	Aorta
20	chr12:2227800-2231800	Weak transcription	NH-A	brain
21	chr12:2227800-2235800	Weak transcription	Fetal Kidney	kidney
22	chr12:2228000-2229400	Weak transcription	Fetal Heart	heart
23	chr12:2228000-2230200	Enhancers	Fetal Stomach	stomach
24	chr12:2228000-2230800	Enhancers	Colon Smooth Muscle	Colon
25	chr12:2228000-2234200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr12:2228000-2235800	Weak transcription	Brain Angular Gyrus	brain
27	chr12:2228200-2229200	Enhancers	Fetal Intestine Small	intestine
28	chr12:2228200-2229200	Enhancers	Fetal Muscle Trunk	muscle
29	chr12:2228200-2230400	Enhancers	Fetal Muscle Leg	muscle
30	chr12:2228400-2229200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
31	chr12:2228400-2229600	Enhancers	NHLF	lung
32	chr12:2228400-2230400	Enhancers	Ovary	ovary
33	chr12:2228400-2230400	Enhancers	NHDF-Ad	bronchial
34	chr12:2228400-2232000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:2228600-2229200	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr12:2228600-2229800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:2228600-2229800	Weak transcription	Right Ventricle	heart
38	chr12:2228600-2235200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr12:2228800-2229800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:2228800-2229800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:2228800-2229800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:2228800-2234200	Weak transcription	Right Atrium	heart
43	chr12:2229000-2229200	Enhancers	Esophagus	oesophagus
44	chr12:2229000-2229400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr12:2229000-2229400	Enhancers	Osteobl	bone
46	chr12:2229000-2229600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:2229000-2231800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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