Variant report

Variant	rs58619945
Chromosome Location	chr12:2160825-2160826
allele	A/G
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	MXI1	chr12:2160712-2163895	IMR90	lung:	n/a	n/a
2	RAD21	chr12:2160647-2161822	SK-N-SH	brain:	n/a	chr12:2161220-2161239
3	ZMIZ1	chr12:2160824-2160851	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:2144090..2145938-chr12:2158684..2161227,2	MCF-7	breast:

Variant related genes	Relation type
CACNA1C	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12422291	0.98[ASN][1000 genomes]
rs2108634	0.98[ASN][1000 genomes]
rs2299656	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3794304	0.89[ASN][1000 genomes]
rs4765879	0.91[EUR][1000 genomes]
rs4765880	0.88[EUR][1000 genomes]
rs59149107	0.91[EUR][1000 genomes]
rs60208923	0.91[EUR][1000 genomes]
rs60312080	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61174808	0.91[EUR][1000 genomes]
rs7301484	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs765124	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	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	nsv898598	chr12:1939252-2215448	Strong transcription Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv898601	chr12:2124955-2215448	Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv826182	chr12:2136395-2208074	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	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
13	nsv898602	chr12:2149786-2223740	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2158800-2161200	Enhancers	Fetal Heart	heart
2	chr12:2159400-2161000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:2159400-2161200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:2159600-2161000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:2159800-2161000	Weak transcription	Osteobl	bone
6	chr12:2160200-2161200	Enhancers	HSMMtube	muscle
7	chr12:2160600-2161000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
8	chr12:2160600-2161000	Enhancers	Left Ventricle	heart
9	chr12:2160600-2161000	Enhancers	Stomach Smooth Muscle	stomach
10	chr12:2160600-2161000	Enhancers	Spleen	Spleen
11	chr12:2160600-2161200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:2160600-2161200	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr12:2160600-2161400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
14	chr12:2160800-2161000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:2160800-2161000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr12:2160800-2161000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:2160800-2161000	Enhancers	Brain Anterior Caudate	brain
18	chr12:2160800-2161000	Bivalent Enhancer	Fetal Brain Female	brain
19	chr12:2160800-2161000	Bivalent Enhancer	Fetal Lung	lung
20	chr12:2160800-2161000	Enhancers	Placenta Amnion	Placenta Amnion
21	chr12:2160800-2161200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
22	chr12:2160800-2161200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr12:2160800-2161200	Bivalent Enhancer	Fetal Intestine Large	intestine
24	chr12:2160800-2161200	Bivalent Enhancer	Fetal Stomach	stomach
25	chr12:2160800-2161200	Enhancers	Right Ventricle	heart
26	chr12:2160800-2161200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
27	chr12:2160800-2161400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:2160800-2161400	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:2160800-2161400	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
30	chr12:2160800-2161400	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr12:2160800-2161400	Flanking Bivalent TSS/Enh	Rectal Smooth Muscle	rectum
32	chr12:2160800-2164200	Active TSS	NHDF-Ad	bronchial
33	chr12:2160800-2166200	Active TSS	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links