Variant report

Variant	rs360800
Chromosome Location	chr2:62954326-62954327
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MEF2A	chr2:62954302-62954809	GM12878	blood:	n/a	n/a
2	NFIC	chr2:62954323-62954869	GM12878	blood:	n/a	n/a
3	RUNX3	chr2:62954310-62954901	GM12878	blood:	n/a	n/a

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

Variant related genes	Relation type
ENSG00000252436	TF binding region
ENSG00000233702	Chromatin interaction
ENSG00000186889	Chromatin interaction
ENSG00000115504	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10153716	0.83[EUR][1000 genomes]
rs10168771	0.80[ASN][1000 genomes]
rs1022110	0.96[CEU][hapmap]
rs11682530	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[ASN][1000 genomes]
rs11688816	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11893131	0.92[CEU][hapmap]
rs12328837	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs12713467	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12713468	0.96[CEU][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12713469	0.85[CHB][hapmap];0.91[CHD][hapmap]
rs12989754	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12994674	0.89[ASN][1000 genomes]
rs13013218	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1386399	0.87[JPT][hapmap]
rs1420018	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1487074	0.81[CHD][hapmap];0.93[JPT][hapmap]
rs1534418	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs1534420	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs1553832	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17027429	0.88[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap]
rs1828398	0.88[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];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1906198	0.83[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2058566	0.81[ASN][1000 genomes]
rs2136737	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2204655	0.87[JPT][hapmap]
rs2204656	0.87[JPT][hapmap]
rs2215870	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[ASN][1000 genomes]
rs2421816	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[GIH][hapmap];0.92[LWK][hapmap];0.96[TSI][hapmap]
rs2430388	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs2539985	0.82[ASN][1000 genomes]
rs2539987	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.84[TSI][hapmap]
rs2710638	0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2710639	0.88[CEU][hapmap]
rs2710640	0.82[ASN][1000 genomes]
rs2710642	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34104251	0.83[EUR][1000 genomes]
rs360797	0.87[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs360799	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	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360807	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs360808	0.84[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs3927201	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4461246	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671050	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[EUR][1000 genomes]
rs4671448	0.90[CHB][hapmap]
rs4671450	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545968	0.93[JPT][hapmap]
rs6545969	0.82[CHD][hapmap];0.93[JPT][hapmap]
rs6545971	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6545972	0.88[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap]
rs6545973	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[GIH][hapmap];0.92[LWK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6705835	0.93[JPT][hapmap]
rs6757128	0.93[JPT][hapmap]
rs7557501	0.88[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap]
rs7562149	0.92[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs7562734	0.80[EUR][1000 genomes]
rs7567923	0.88[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap]
rs7573756	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9678329	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9973612	0.92[CEU][hapmap];0.82[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:102 , 50 per page) page: 1 2 3

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	chr2:62950200-62957800	Weak transcription	Fetal Lung	lung
26	chr2:62950200-62957800	Weak transcription	HSMM	muscle
27	chr2:62950400-62957800	Weak transcription	Fetal Intestine Large	intestine
28	chr2:62950400-62957800	Weak transcription	Dnd41	blood
29	chr2:62950600-62957800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:62950600-62957800	Weak transcription	Fetal Muscle Leg	muscle
31	chr2:62950600-62960600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:62950800-62957800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:62951200-62957800	Weak transcription	Primary T cells from cord blood	blood
34	chr2:62952200-62957400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:62952200-62957800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:62952400-62954400	Weak transcription	Fetal Heart	heart
37	chr2:62952600-62954800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:62952600-62955000	Genic enhancers	HepG2	liver
39	chr2:62952600-62957800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr2:62952600-62957800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr2:62952600-62957800	Weak transcription	Fetal Brain Male	brain
42	chr2:62952800-62955400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:62952800-62957800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:62952800-62957800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:62952800-62957800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr2:62952800-62960600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:62953000-62955000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:62953000-62957800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:62953000-62957800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:62953000-62957800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links