Variant report

Variant	rs62557474
Chromosome Location	chr9:100177557-100177558
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100176159..100177806-chr9:100179325..100182162,2	MCF-7	breast:
2	chr9:100174630..100178511-chr9:100198260..100202399,3	K562	blood:
3	chr9:100173722..100176324-chr9:100177093..100182723,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196116	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11999505	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12001521	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12002057	0.91[EUR][1000 genomes]
rs12003293	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12006001	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16920147	0.98[ASN][1000 genomes]
rs16920171	0.98[ASN][1000 genomes]
rs16920185	0.91[EUR][1000 genomes]
rs16920387	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16920392	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16920394	0.86[ASN][1000 genomes]
rs16920403	0.86[ASN][1000 genomes]
rs16920407	0.86[ASN][1000 genomes]
rs16920414	0.86[ASN][1000 genomes]
rs16920418	0.86[ASN][1000 genomes]
rs35600334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41281938	0.91[EUR][1000 genomes]
rs58008468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58099598	0.82[EUR][1000 genomes]
rs59749998	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59837265	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60023110	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61418045	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62557475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62557493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62557494	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62557495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62557498	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62557499	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62557500	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62557501	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62557502	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62557510	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62557511	0.91[EUR][1000 genomes]
rs62557512	0.91[EUR][1000 genomes]
rs62557513	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62557542	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62557544	0.91[EUR][1000 genomes]
rs62557545	0.91[EUR][1000 genomes]
rs62557546	0.91[EUR][1000 genomes]
rs62557548	0.91[EUR][1000 genomes]
rs62557551	0.87[EUR][1000 genomes]
rs62557552	0.87[EUR][1000 genomes]
rs62557553	0.87[EUR][1000 genomes]
rs7024030	0.91[EUR][1000 genomes]
rs7044475	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7048438	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs732688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7853578	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7871235	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893609	chr9:100163998-100297592	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv982177	chr9:100177309-100178919	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100175200-100179400	Weak transcription	Lung	lung
2	chr9:100175200-100180800	Weak transcription	Esophagus	oesophagus
3	chr9:100175400-100177800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr9:100175400-100177800	Enhancers	Liver	Liver
5	chr9:100175400-100190400	Weak transcription	Aorta	Aorta
6	chr9:100175400-100190800	Weak transcription	Left Ventricle	heart
7	chr9:100175400-100230800	Weak transcription	Psoas Muscle	Psoas
8	chr9:100175600-100178000	Enhancers	Fetal Intestine Large	intestine
9	chr9:100175600-100178400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:100175600-100181000	Weak transcription	HUVEC	blood vessel
11	chr9:100175600-100189600	Weak transcription	Primary T cells from cord blood	blood
12	chr9:100175600-100191200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:100175600-100202600	Weak transcription	Fetal Muscle Leg	muscle
14	chr9:100175600-100245200	Weak transcription	Right Ventricle	heart
15	chr9:100175800-100181200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr9:100175800-100181400	Weak transcription	HSMM	muscle
17	chr9:100176000-100177600	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr9:100176000-100180800	Weak transcription	Stomach Mucosa	stomach
19	chr9:100176000-100181000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:100176000-100181200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:100176000-100181200	Weak transcription	NHDF-Ad	bronchial
22	chr9:100176000-100181400	Weak transcription	A549	lung
23	chr9:100176000-100181400	Weak transcription	NHLF	lung
24	chr9:100176000-100183200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr9:100176000-100191200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr9:100176200-100177600	Weak transcription	Small Intestine	intestine
27	chr9:100176200-100177600	Enhancers	HepG2	liver
28	chr9:100176200-100178000	Enhancers	Fetal Intestine Small	intestine
29	chr9:100176200-100178200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr9:100176200-100179200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr9:100176200-100179200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr9:100176200-100179800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:100176200-100180200	Weak transcription	Primary B cells from cord blood	blood
34	chr9:100176200-100180200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr9:100176200-100180600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr9:100176200-100180800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr9:100176200-100180800	Weak transcription	Colonic Mucosa	Colon
38	chr9:100176200-100181000	Weak transcription	Pancreas	Pancrea
39	chr9:100176200-100181200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr9:100176200-100181400	Weak transcription	Colon Smooth Muscle	Colon
41	chr9:100176200-100182800	Weak transcription	Fetal Brain Female	brain
42	chr9:100176200-100185400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr9:100176200-100190400	Weak transcription	Spleen	Spleen
44	chr9:100176200-100194400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr9:100176200-100203000	Weak transcription	Dnd41	blood
46	chr9:100176400-100192000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr9:100176600-100180200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr9:100176600-100180600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr9:100176600-100181000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr9:100176600-100181400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links