Variant report

Variant	rs360799
Chromosome Location	chr2:62953166-62953167
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:62931218..62935918-chr2:62951550..62955731,6	MCF-7	breast:
2	chr2:62733287..62736036-chr2:62952497..62954456,3	MCF-7	breast:
3	chr2:62683825..62684898-chr2:62951738..62953509,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186889	Chromatin interaction
ENSG00000115504	Chromatin interaction
ENSG00000233702	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10153716	0.82[EUR][1000 genomes]
rs10168771	0.80[ASN][1000 genomes]
rs1022110	0.87[CEU][hapmap]
rs11682530	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs11688816	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11893131	0.91[CEU][hapmap];0.84[YRI][hapmap]
rs12328837	0.93[JPT][hapmap];0.91[YRI][hapmap];0.80[ASN][1000 genomes]
rs12713467	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12713468	0.96[CEU][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12713469	0.85[CHB][hapmap]
rs12989754	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12994674	0.89[ASN][1000 genomes]
rs13013218	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13398408	0.82[YRI][hapmap]
rs13418889	0.81[AFR][1000 genomes]
rs1386399	0.87[JPT][hapmap]
rs1386401	0.87[YRI][hapmap]
rs1420018	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1487074	0.93[JPT][hapmap]
rs1534418	0.87[JPT][hapmap]
rs1534420	0.87[JPT][hapmap]
rs1553832	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17027429	0.87[CEU][hapmap];0.94[GIH][hapmap];0.88[LWK][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs1828398	0.87[CEU][hapmap]
rs1872789	0.87[JPT][hapmap]
rs1872790	0.93[JPT][hapmap]
rs189671	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1906198	0.83[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2058566	0.81[ASN][1000 genomes]
rs2080227	0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs2136737	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2204655	0.87[JPT][hapmap]
rs2204656	0.87[JPT][hapmap]
rs2215870	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[ASN][1000 genomes]
rs2421816	0.83[CEU][hapmap];0.90[GIH][hapmap]
rs2430388	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[YRI][hapmap]
rs2539985	0.82[ASN][1000 genomes]
rs2539987	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap]
rs2710638	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2710640	0.82[ASN][1000 genomes]
rs2710642	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs34104251	0.82[EUR][1000 genomes]
rs360797	0.87[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs360800	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360801	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs360804	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360807	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs360808	0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs3927201	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4461246	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4671050	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4671448	0.90[CHB][hapmap]
rs4671450	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545968	0.93[JPT][hapmap]
rs6545969	0.93[JPT][hapmap];0.95[YRI][hapmap]
rs6545971	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6545972	0.87[CEU][hapmap];0.94[GIH][hapmap];0.83[LWK][hapmap];0.83[YRI][hapmap]
rs6545973	0.83[CEU][hapmap];0.90[GIH][hapmap]
rs6705835	0.93[JPT][hapmap]
rs6757128	0.93[JPT][hapmap];0.95[YRI][hapmap]
rs7557501	0.87[CEU][hapmap];0.94[GIH][hapmap];0.83[LWK][hapmap];0.91[YRI][hapmap]
rs7562149	0.91[CEU][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];0.81[EUR][1000 genomes]
rs7567923	0.87[CEU][hapmap];0.94[GIH][hapmap];0.88[LWK][hapmap];0.91[YRI][hapmap]
rs7573756	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9678329	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9973612	0.91[CEU][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62934200-62957800	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:62934200-62957800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:62934400-62957800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr2:62934600-62957800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:62934600-62957800	Weak transcription	Thymus	Thymus
6	chr2:62934600-62957800	Weak transcription	HSMMtube	muscle
7	chr2:62935800-62957800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:62936200-62957800	Weak transcription	Small Intestine	intestine
9	chr2:62936400-62957800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:62936400-62957800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:62936600-62957800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:62936600-62957800	Weak transcription	Hela-S3	cervix
13	chr2:62937200-62957800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr2:62937200-62957800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:62937400-62957800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr2:62938600-62957800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:62941800-62957800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:62944000-62957800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:62944000-62957800	Weak transcription	Aorta	Aorta
20	chr2:62944200-62957800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:62944400-62957800	Weak transcription	NHEK	skin
22	chr2:62944600-62957800	Weak transcription	NH-A	brain
23	chr2:62945800-62957800	Weak transcription	NHLF	lung
24	chr2:62946800-62957800	Weak transcription	HMEC	breast
25	chr2:62949400-62953600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:62949800-62953600	Enhancers	Liver	Liver
27	chr2:62950200-62957800	Weak transcription	Fetal Lung	lung
28	chr2:62950200-62957800	Weak transcription	HSMM	muscle
29	chr2:62950400-62957800	Weak transcription	Fetal Intestine Large	intestine
30	chr2:62950400-62957800	Weak transcription	Dnd41	blood
31	chr2:62950600-62957800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:62950600-62957800	Weak transcription	Fetal Muscle Leg	muscle
33	chr2:62950600-62960600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:62950800-62957800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:62951200-62953200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:62951200-62957800	Weak transcription	Primary T cells from cord blood	blood
37	chr2:62951400-62953400	Enhancers	Adipose Nuclei	Adipose
38	chr2:62951600-62953200	Enhancers	H9 Cell Line	embryonic stem cell
39	chr2:62951600-62953200	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr2:62951600-62953400	Enhancers	Brain Angular Gyrus	brain
41	chr2:62951600-62953800	Enhancers	Rectal Smooth Muscle	rectum
42	chr2:62951800-62953200	Enhancers	H1 Cell Line	embryonic stem cell
43	chr2:62951800-62953200	Enhancers	Brain Hippocampus Middle	brain
44	chr2:62951800-62953200	Enhancers	Left Ventricle	heart
45	chr2:62951800-62953200	Enhancers	Spleen	Spleen
46	chr2:62951800-62953400	Enhancers	Brain Cingulate Gyrus	brain
47	chr2:62951800-62953400	Genic enhancers	Esophagus	oesophagus
48	chr2:62951800-62953400	Enhancers	Pancreas	Pancrea
49	chr2:62951800-62953400	Enhancers	Right Atrium	heart
50	chr2:62951800-62953600	Strong transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links