Variant report

Variant	rs7601625
Chromosome Location	chr2:55251374-55251375
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55245011..55247166-chr2:55250682..55252602,2	MCF-7	breast:
2	chr2:55243166..55246645-chr2:55249862..55254918,6	K562	blood:
3	chr2:55248265..55251849-chr2:55275117..55277756,4	MCF-7	breast:
4	chr2:55247845..55251421-chr2:55399362..55401204,3	K562	blood:
5	chr2:55251258..55253325-chr2:55261770..55263673,2	K562	blood:
6	chr2:55238125..55242197-chr2:55249599..55253048,4	K562	blood:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction
ENSG00000200086	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10170340	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10189379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10210840	0.82[YRI][hapmap]
rs10496036	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10496037	0.90[CHB][hapmap]
rs12464447	0.86[ASN][1000 genomes]
rs12464595	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12469804	0.90[CHB][hapmap]
rs12475787	0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs12475904	0.89[ASN][1000 genomes]
rs12479297	0.90[ASN][1000 genomes]
rs1348528	1.00[CHB][hapmap]
rs17046570	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17046594	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17347089	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17418675	1.00[JPT][hapmap]
rs1822618	1.00[CHB][hapmap]
rs2864049	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55993793	0.82[ASN][1000 genomes]
rs56013263	0.87[ASN][1000 genomes]
rs6545467	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6713935	0.90[CHB][hapmap]
rs67156582	0.85[ASN][1000 genomes]
rs6730728	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72795440	0.97[ASN][1000 genomes]
rs7584354	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7584386	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs887	0.90[JPT][hapmap]

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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
2	chr2:55237600-55258600	Weak transcription	Ovary	ovary
3	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
4	chr2:55238400-55252200	Weak transcription	Fetal Thymus	thymus
5	chr2:55238400-55252400	Weak transcription	Thymus	Thymus
6	chr2:55238400-55253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:55241000-55272400	Weak transcription	Fetal Kidney	kidney
8	chr2:55241400-55253400	Weak transcription	Fetal Lung	lung
9	chr2:55242000-55252400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:55242200-55253400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:55242400-55253400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:55242400-55258000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:55243000-55262400	Weak transcription	Hela-S3	cervix
14	chr2:55243200-55252600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:55243800-55259800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:55245000-55256000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:55245400-55253400	Weak transcription	Liver	Liver
18	chr2:55245600-55265600	Weak transcription	Stomach Mucosa	stomach
19	chr2:55246400-55254000	Enhancers	Brain Substantia Nigra	brain
20	chr2:55246800-55251600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr2:55246800-55259800	Weak transcription	NH-A	brain
22	chr2:55247200-55251400	Enhancers	Brain Hippocampus Middle	brain
23	chr2:55247200-55252200	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr2:55247400-55252200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:55247600-55251600	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr2:55247800-55251600	Genic enhancers	K562	blood
27	chr2:55248200-55252200	Enhancers	HUVEC	blood vessel
28	chr2:55248200-55253200	Weak transcription	Fetal Intestine Large	intestine
29	chr2:55248200-55253600	Weak transcription	Fetal Intestine Small	intestine
30	chr2:55248200-55253800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:55248200-55255200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:55248200-55255200	Weak transcription	Left Ventricle	heart
33	chr2:55248200-55258400	Weak transcription	Lung	lung
34	chr2:55248200-55259200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:55248400-55251400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:55248600-55251600	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr2:55248600-55251600	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr2:55248600-55256400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr2:55248800-55252200	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:55249000-55252000	Weak transcription	Fetal Brain Female	brain
41	chr2:55249000-55256200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr2:55249000-55256600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:55249000-55256600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr2:55249000-55256600	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr2:55249000-55256600	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr2:55249200-55251400	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr2:55249200-55251400	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr2:55249200-55251800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:55249200-55252200	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr2:55249200-55255000	Strong transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links