Variant report

Variant	rs2870780
Chromosome Location	chr12:66680302-66680303
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:66679445..66683065-chr12:66693885..66696538,3	K562	blood:

Variant related genes	Relation type
ENSG00000127311	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10784521	0.88[EUR][1000 genomes]
rs10878402	0.84[CHB][hapmap]
rs11176137	0.85[CHB][hapmap]
rs11176142	0.88[CHB][hapmap]
rs11610967	0.88[CHB][hapmap]
rs12819421	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2043668	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs289058	1.00[CEU][hapmap]
rs289059	0.92[EUR][1000 genomes]
rs289061	1.00[CEU][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]
rs289066	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs3741604	0.84[CHB][hapmap]
rs4382951	0.87[EUR][1000 genomes]
rs6421217	0.88[CHB][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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899216	chr12:66563835-66716844	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2870780	HELB	cis	parietal	SCAN
rs2870780	IFNG	cis	parietal	SCAN
rs2870780	HELB	Cis_1M	lymphoblastoid	RTeQTL
rs2870780	HELB	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66673600-66680400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:66676600-66681400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr12:66676800-66681600	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr12:66677000-66681400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr12:66677200-66681600	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr12:66678200-66684400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:66679000-66681600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr12:66679200-66681400	Enhancers	Primary T cells from cord blood	blood
9	chr12:66679400-66681600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:66679400-66681800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr12:66679600-66681600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr12:66679600-66682000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:66679800-66681400	Enhancers	Dnd41	blood
14	chr12:66679800-66681600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr12:66680000-66680400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:66680000-66681600	Enhancers	Thymus	Thymus
17	chr12:66680000-66685600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:66680000-66685600	Enhancers	Fetal Thymus	thymus
19	chr12:66680200-66681400	Weak transcription	K562	blood
20	chr12:66680200-66689400	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links