Variant report

Variant	rs1558321
Chromosome Location	chr12:2230320-2230321
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:28)

rs_ID	r²[population]
rs1005618	0.85[ASN][1000 genomes]
rs10848617	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1122864	0.92[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1558322	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2238027	0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2238029	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2238033	0.91[EUR][1000 genomes]
rs2238034	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2238036	0.83[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2239130	0.91[EUR][1000 genomes]
rs2239131	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]
rs2239133	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2239134	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2239135	0.89[EUR][1000 genomes]
rs2247833	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2283283	0.87[MEX][hapmap]
rs2299660	0.85[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2299661	0.91[EUR][1000 genomes]
rs2299662	0.90[EUR][1000 genomes]
rs2299663	0.95[EUR][1000 genomes]
rs2299664	1.00[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs4126711	0.91[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs4765897	0.89[EUR][1000 genomes]
rs4765898	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs6489348	0.91[MEX][hapmap]
rs758723	0.91[EUR][1000 genomes]
rs874924	0.88[EUR][1000 genomes]
rs881303	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][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	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
19	nsv1041632	chr12:2230012-2257585	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv557037	chr12:2230055-2257916	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1558321	KCNA1	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2219000-2234000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:2220800-2235400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:2222000-2231200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:2222000-2235400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:2222400-2239000	Weak transcription	Brain Anterior Caudate	brain
6	chr12:2222800-2236000	Weak transcription	Lung	lung
7	chr12:2223200-2250200	Weak transcription	Brain Substantia Nigra	brain
8	chr12:2223400-2234000	Weak transcription	Spleen	Spleen
9	chr12:2223600-2238200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:2224400-2231000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:2224600-2231200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:2225400-2233800	Weak transcription	Fetal Brain Female	brain
13	chr12:2226800-2231200	Enhancers	Rectal Smooth Muscle	rectum
14	chr12:2227400-2231600	Enhancers	Fetal Lung	lung
15	chr12:2227600-2230600	Enhancers	Aorta	Aorta
16	chr12:2227800-2231800	Weak transcription	NH-A	brain
17	chr12:2227800-2235800	Weak transcription	Fetal Kidney	kidney
18	chr12:2228000-2230800	Enhancers	Colon Smooth Muscle	Colon
19	chr12:2228000-2234200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:2228000-2235800	Weak transcription	Brain Angular Gyrus	brain
21	chr12:2228200-2230400	Enhancers	Fetal Muscle Leg	muscle
22	chr12:2228400-2230400	Enhancers	Ovary	ovary
23	chr12:2228400-2230400	Enhancers	NHDF-Ad	bronchial
24	chr12:2228400-2232000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:2228600-2235200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:2228800-2234200	Weak transcription	Right Atrium	heart
27	chr12:2229000-2231800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:2229200-2231200	Weak transcription	Fetal Intestine Small	intestine
29	chr12:2229400-2230400	Enhancers	Fetal Heart	heart
30	chr12:2229400-2230600	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr12:2229600-2230400	Genic enhancers	Left Ventricle	heart
32	chr12:2229600-2231800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:2229800-2230400	Enhancers	Right Ventricle	heart
34	chr12:2229800-2230600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:2229800-2231800	Strong transcription	Osteobl	bone
36	chr12:2229800-2232000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:2229800-2237200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:2229800-2245600	Weak transcription	Stomach Mucosa	stomach
39	chr12:2230000-2233200	Weak transcription	Fetal Brain Male	brain
40	chr12:2230200-2230600	Genic enhancers	NHLF	lung
41	chr12:2230200-2230800	Enhancers	Stomach Smooth Muscle	stomach
42	chr12:2230200-2231600	Genic enhancers	Fetal Stomach	stomach

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