Variant report

Variant	rs12621527
Chromosome Location	chr2:20782915-20782916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20782430..20784045-chr2:20806055..20808351,2	K562	blood:
2	chr2:20777247..20781087-chr2:20782458..20786081,5	K562	blood:
3	chr2:20723966..20726064-chr2:20781037..20784035,2	K562	blood:
4	chr2:20645526..20651779-chr2:20782666..20787622,12	MCF-7	breast:
5	chr2:20772999..20776929-chr2:20778925..20783592,5	MCF-7	breast:
6	chr2:20778242..20781356-chr2:20782083..20785108,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143878	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000233416	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10166792	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10177787	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10177834	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs10190705	0.84[ASN][1000 genomes]
rs10195324	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10195722	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10200207	0.83[ASN][1000 genomes]
rs11096676	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11096677	0.87[ASN][1000 genomes]
rs11096679	0.86[CHB][hapmap]
rs1123781	0.88[ASN][1000 genomes]
rs11691255	0.84[ASN][1000 genomes]
rs11885969	0.86[CHB][hapmap]
rs11897611	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12472478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13013281	0.86[CHB][hapmap]
rs13031724	0.86[CHB][hapmap]
rs13032956	0.81[CHB][hapmap]
rs13422371	0.84[ASN][1000 genomes]
rs16987857	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16987878	0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs16987880	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs16987884	0.93[JPT][hapmap]
rs2882035	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2882036	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4666315	0.87[ASN][1000 genomes]
rs4666426	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4666427	0.93[ASN][1000 genomes]
rs4666428	0.87[EUR][1000 genomes]
rs4666429	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4666430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4666431	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4666436	0.86[CHB][hapmap]
rs55835545	0.80[ASN][1000 genomes]
rs56129345	0.84[ASN][1000 genomes]
rs6715159	0.86[CHB][hapmap]
rs6722960	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs72782365	0.83[ASN][1000 genomes]
rs72782368	0.80[ASN][1000 genomes]
rs766474	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs921599	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs921601	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12621527		cis	Lymphoblastoid	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20765800-20786200	Enhancers	HUVEC	blood vessel
2	chr2:20772600-20785800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:20778800-20784800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:20779600-20783600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr2:20779600-20783800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:20779800-20783600	Weak transcription	Fetal Kidney	kidney
7	chr2:20779800-20783800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:20779800-20784000	Enhancers	HepG2	liver
9	chr2:20780000-20783600	Weak transcription	Osteobl	bone
10	chr2:20780000-20783800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:20780000-20783800	Weak transcription	Ovary	ovary
12	chr2:20780000-20784000	Weak transcription	Aorta	Aorta
13	chr2:20780000-20784200	Weak transcription	Psoas Muscle	Psoas
14	chr2:20780000-20784200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:20780000-20784400	Weak transcription	Colonic Mucosa	Colon
16	chr2:20780000-20786000	Weak transcription	Small Intestine	intestine
17	chr2:20780200-20783400	Weak transcription	NHDF-Ad	bronchial
18	chr2:20780800-20783600	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:20780800-20784000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:20781200-20784200	Weak transcription	Liver	Liver
21	chr2:20781600-20785400	Enhancers	Placenta Amnion	Placenta Amnion
22	chr2:20781600-20786000	Enhancers	Brain Hippocampus Middle	brain
23	chr2:20781800-20786000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr2:20781800-20786000	Enhancers	Brain Anterior Caudate	brain
25	chr2:20781800-20786000	Enhancers	Brain Substantia Nigra	brain
26	chr2:20781800-20786200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:20781800-20786800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:20782000-20783400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:20782000-20783600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:20782000-20783800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:20782000-20784000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:20782000-20785400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:20782000-20785800	Enhancers	Brain Angular Gyrus	brain
34	chr2:20782000-20785800	Enhancers	K562	blood
35	chr2:20782000-20786000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:20782000-20786200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:20782000-20786200	Enhancers	Fetal Intestine Small	intestine
38	chr2:20782000-20787400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr2:20782200-20783200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:20782200-20784000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:20782200-20786200	Enhancers	Placenta	Placenta
42	chr2:20782200-20786400	Enhancers	Fetal Stomach	stomach
43	chr2:20782400-20785600	Enhancers	Fetal Intestine Large	intestine
44	chr2:20782400-20785800	Enhancers	Brain Cingulate Gyrus	brain
45	chr2:20782400-20786000	Enhancers	Left Ventricle	heart
46	chr2:20782400-20786000	Enhancers	Pancreas	Pancrea
47	chr2:20782400-20786000	Enhancers	Right Ventricle	heart
48	chr2:20782400-20786400	Enhancers	Right Atrium	heart
49	chr2:20782400-20786400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr2:20782600-20783000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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