Variant report

Variant	rs360804
Chromosome Location	chr2:62939397-62939398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:62931680..62936564-chr2:62937954..62947758,18	K562	blood:

Variant related genes	Relation type
ENSG00000115504	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
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];0.84[MEX][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	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12713468	0.96[CEU][hapmap];0.84[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];0.86[MEX][hapmap];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];0.89[ASN][1000 genomes]
rs1386399	0.87[JPT][hapmap]
rs1420018	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17027429	0.88[CEU][hapmap];0.90[GIH][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];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1906198	0.83[ASW][hapmap];0.83[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.86[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];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2204655	0.87[JPT][hapmap]
rs2204656	0.87[JPT][hapmap]
rs2215870	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs2421816	0.92[CEU][hapmap];0.93[GIH][hapmap]
rs2430388	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs2539985	0.82[ASN][1000 genomes]
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	0.82[ASN][1000 genomes]
rs360797	0.87[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.92[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];0.81[MEX][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360800	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]
rs360801	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360807	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs360808	0.84[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs3927201	0.88[ASN][1000 genomes]
rs4461246	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4671050	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs4671448	0.90[CHB][hapmap]
rs4671450	0.85[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];0.90[GIH][hapmap]
rs6545973	0.92[CEU][hapmap];0.93[GIH][hapmap]
rs6705835	0.93[JPT][hapmap]
rs6757128	0.93[JPT][hapmap]
rs7557501	0.88[CEU][hapmap];0.90[GIH][hapmap]
rs7562149	0.92[CEU][hapmap];0.87[GIH][hapmap]
rs7567923	0.88[CEU][hapmap];0.90[GIH][hapmap]
rs7573756	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9678329	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9973612	0.92[CEU][hapmap]

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:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62934200-62945800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:62934200-62957800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:62934200-62957800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:62934400-62939800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:62934400-62957800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr2:62934600-62940600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:62934600-62942200	Weak transcription	Spleen	Spleen
8	chr2:62934600-62943800	Weak transcription	Aorta	Aorta
9	chr2:62934600-62945000	Weak transcription	Right Ventricle	heart
10	chr2:62934600-62945400	Weak transcription	Fetal Thymus	thymus
11	chr2:62934600-62947400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr2:62934600-62951600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:62934600-62951800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:62934600-62951800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:62934600-62951800	Weak transcription	Esophagus	oesophagus
16	chr2:62934600-62951800	Weak transcription	Left Ventricle	heart
17	chr2:62934600-62952400	Weak transcription	Gastric	stomach
18	chr2:62934600-62957800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:62934600-62957800	Weak transcription	Thymus	Thymus
20	chr2:62934600-62957800	Weak transcription	HSMMtube	muscle
21	chr2:62934800-62939600	Strong transcription	HSMM	muscle
22	chr2:62934800-62951800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:62935000-62948400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:62935200-62943200	Weak transcription	HUVEC	blood vessel
25	chr2:62935200-62949000	Weak transcription	Fetal Intestine Large	intestine
26	chr2:62935400-62939400	ZNF genes & repeats	NHLF	lung
27	chr2:62935600-62939400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:62935600-62939800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:62935600-62940000	ZNF genes & repeats	GM12878-XiMat	blood
30	chr2:62935600-62941200	ZNF genes & repeats	NHDF-Ad	bronchial
31	chr2:62935600-62943400	Strong transcription	Primary hematopoietic stem cells	blood
32	chr2:62935800-62939400	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr2:62935800-62939400	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:62935800-62943600	Weak transcription	Fetal Stomach	stomach
35	chr2:62935800-62957800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:62936000-62942800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:62936000-62943400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:62936000-62951800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr2:62936200-62939400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr2:62936200-62939400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:62936200-62944400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:62936200-62950200	Weak transcription	Brain Anterior Caudate	brain
43	chr2:62936200-62957800	Weak transcription	Small Intestine	intestine
44	chr2:62936400-62939600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:62936400-62940000	ZNF genes & repeats	A549	lung
46	chr2:62936400-62942200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:62936400-62943800	Weak transcription	Fetal Intestine Small	intestine
48	chr2:62936400-62943800	Weak transcription	Psoas Muscle	Psoas
49	chr2:62936400-62943800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:62936400-62949800	Weak transcription	Fetal Lung	lung

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