Variant report

Variant	rs973504
Chromosome Location	chr2:231293870-231293871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:231292538..231294481-chr2:231296782..231298607,2	MCF-7	breast:
2	chr2:231292379..231294379-chr2:231300867..231302513,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10180055	0.93[ASN][1000 genomes]
rs10180131	0.95[ASN][1000 genomes]
rs10191049	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10207311	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10804365	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11682084	0.93[ASN][1000 genomes]
rs11688912	0.91[ASN][1000 genomes]
rs11689240	0.95[ASN][1000 genomes]
rs11690286	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11898168	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13411346	0.93[ASN][1000 genomes]
rs13411566	0.97[ASN][1000 genomes]
rs3754944	0.96[ASN][1000 genomes]
rs4142872	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56102622	0.93[ASN][1000 genomes]
rs56377716	0.92[ASN][1000 genomes]
rs62193378	0.93[ASN][1000 genomes]
rs62193388	0.93[ASN][1000 genomes]
rs6436937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6722012	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730329	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6748062	0.97[ASN][1000 genomes]
rs6748069	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6756448	0.96[ASN][1000 genomes]
rs7581828	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7582700	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7595408	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][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	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv584672	chr2:231289976-231348888	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231281600-231294800	Weak transcription	Gastric	stomach
2	chr2:231282000-231294000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:231283600-231294800	Weak transcription	HSMM	muscle
4	chr2:231283600-231309200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:231283800-231294600	Weak transcription	Fetal Heart	heart
6	chr2:231283800-231294800	Weak transcription	Esophagus	oesophagus
7	chr2:231284200-231294800	Weak transcription	Lung	lung
8	chr2:231284200-231294800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:231284200-231294800	Weak transcription	Thymus	Thymus
10	chr2:231284200-231301000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:231284200-231304000	Weak transcription	NH-A	brain
12	chr2:231284600-231306200	Weak transcription	HMEC	breast
13	chr2:231288800-231319000	Weak transcription	Fetal Kidney	kidney
14	chr2:231288800-231356000	Weak transcription	Stomach Mucosa	stomach
15	chr2:231289000-231294000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr2:231289000-231294800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:231289000-231295000	Weak transcription	Right Ventricle	heart
18	chr2:231289000-231299400	Weak transcription	NHLF	lung
19	chr2:231289000-231309200	Weak transcription	Aorta	Aorta
20	chr2:231289200-231294800	Weak transcription	Adipose Nuclei	Adipose
21	chr2:231289200-231294800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:231289600-231294800	Weak transcription	Ovary	ovary
23	chr2:231289600-231294800	Weak transcription	Pancreas	Pancrea
24	chr2:231289600-231295400	Weak transcription	Small Intestine	intestine
25	chr2:231290000-231295200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:231290800-231294800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr2:231291000-231295200	ZNF genes & repeats	GM12878-XiMat	blood
28	chr2:231291200-231299600	Weak transcription	NHEK	skin
29	chr2:231291600-231295000	Weak transcription	Hela-S3	cervix
30	chr2:231291800-231294800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:231291800-231294800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:231292000-231294400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:231292000-231294800	Strong transcription	Primary T cells from cord blood	blood
34	chr2:231292200-231294600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:231292200-231294800	Strong transcription	Fetal Thymus	thymus
36	chr2:231292200-231295400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:231292400-231294600	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:231292400-231294800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:231292400-231296200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
40	chr2:231292400-231298400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:231292600-231298800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:231292800-231295800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
43	chr2:231293000-231294000	ZNF genes & repeats	Fetal Intestine Small	intestine
44	chr2:231293000-231294200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
45	chr2:231293000-231294400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
46	chr2:231293000-231295000	Strong transcription	Liver	Liver
47	chr2:231293000-231295400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:231293200-231294000	Strong transcription	HUVEC	blood vessel
49	chr2:231293400-231294000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:231293400-231294000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links