Variant report

Variant	rs12625489
Chromosome Location	chr20:23362825-23362826
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23344681..23346860-chr20:23360081..23363046,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125812	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10485644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076777	0.96[EUR][1000 genomes]
rs1109557	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1122407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12624341	0.98[EUR][1000 genomes]
rs12625187	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12625257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12625297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12625468	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12625948	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12625959	0.96[EUR][1000 genomes]
rs12625994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16985266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs16985303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16985337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2273237	0.96[EUR][1000 genomes]
rs34036626	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34831633	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3736756	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3761276	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs3761278	1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56393556	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56693860	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56725318	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57034369	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs57322153	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57436024	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs57535381	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs57896475	0.98[EUR][1000 genomes]
rs58192622	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59143301	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59852988	0.96[EUR][1000 genomes]
rs60799291	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61024391	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61297472	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61344818	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7265627	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73901826	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73901859	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73901870	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8115832	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8117246	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8123389	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8125332	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448882	chr20:23362387-23362949	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12625489	CSTL1	cis	Esophagus Mucosa	GTEx
rs12625489	CSTL1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23344000-23392600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:23346600-23363200	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr20:23348000-23374200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr20:23348200-23384800	Weak transcription	Stomach Mucosa	stomach
5	chr20:23348600-23363000	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr20:23348800-23363000	Strong transcription	GM12878-XiMat	blood
7	chr20:23348800-23366400	Strong transcription	Dnd41	blood
8	chr20:23349200-23363000	Strong transcription	Adipose Nuclei	Adipose
9	chr20:23349400-23363200	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr20:23349600-23363600	Strong transcription	Liver	Liver
11	chr20:23349600-23366000	Strong transcription	HepG2	liver
12	chr20:23349800-23363000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr20:23349800-23364200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr20:23350000-23363000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr20:23350000-23363600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr20:23351200-23371000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr20:23351200-23374000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr20:23351400-23374000	Weak transcription	Fetal Brain Male	brain
19	chr20:23352200-23367800	Weak transcription	Small Intestine	intestine
20	chr20:23352800-23376400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr20:23353000-23365400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr20:23353000-23378200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr20:23353400-23372400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr20:23353400-23374200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr20:23354400-23389000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr20:23354400-23399800	Weak transcription	Hela-S3	cervix
27	chr20:23354600-23374200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr20:23354600-23375200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr20:23354800-23371000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr20:23354800-23373600	Weak transcription	Colonic Mucosa	Colon
31	chr20:23356600-23365400	Weak transcription	Gastric	stomach
32	chr20:23356600-23374200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr20:23356800-23368800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr20:23357000-23371200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr20:23357200-23364200	Strong transcription	A549	lung
36	chr20:23357400-23363200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr20:23357800-23370000	Weak transcription	Brain Substantia Nigra	brain
38	chr20:23358000-23366800	Weak transcription	K562	blood
39	chr20:23358000-23371200	Weak transcription	Esophagus	oesophagus
40	chr20:23358000-23371200	Weak transcription	NHEK	skin
41	chr20:23358000-23373600	Weak transcription	Right Ventricle	heart
42	chr20:23358000-23374400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr20:23358200-23367800	Weak transcription	NH-A	brain
44	chr20:23358200-23368600	Weak transcription	Fetal Kidney	kidney
45	chr20:23358200-23370600	Weak transcription	Pancreas	Pancrea
46	chr20:23358200-23373600	Weak transcription	Brain Angular Gyrus	brain
47	chr20:23358200-23377800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr20:23358400-23364800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr20:23358400-23370600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr20:23358600-23364000	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links