Variant report

Variant	rs10878397
Chromosome Location	chr12:66676433-66676434
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1009211	0.80[EUR][1000 genomes]
rs10748037	1.00[CEU][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs10784519	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10784520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878396	1.00[CEU][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs10878401	0.80[EUR][1000 genomes]
rs10878402	0.81[CEU][hapmap];0.84[CHB][hapmap];0.80[EUR][1000 genomes]
rs10878403	0.81[CEU][hapmap]
rs11176115	0.89[EUR][1000 genomes]
rs11176117	0.87[EUR][1000 genomes]
rs11176120	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11176125	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs11176126	0.80[EUR][1000 genomes]
rs11176132	0.80[EUR][1000 genomes]
rs11610967	0.88[CHB][hapmap];0.89[YRI][hapmap]
rs1168324	0.98[EUR][1000 genomes]
rs12146776	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12371662	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12423377	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12818303	0.86[EUR][1000 genomes]
rs12819421	0.90[CHB][hapmap]
rs12822967	0.96[EUR][1000 genomes]
rs1603244	0.85[EUR][1000 genomes]
rs1816562	1.00[CEU][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs2047236	0.84[EUR][1000 genomes]
rs2047237	0.87[EUR][1000 genomes]
rs2088169	0.86[EUR][1000 genomes]
rs2118137	0.86[EUR][1000 genomes]
rs289065	0.95[EUR][1000 genomes]
rs2904497	0.81[EUR][1000 genomes]
rs3741604	0.84[CHB][hapmap]
rs6421217	0.83[CEU][hapmap];0.88[CHB][hapmap]
rs6581669	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7137005	0.96[EUR][1000 genomes]
rs7137378	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7138034	0.85[EUR][1000 genomes]
rs724739	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs724742	0.92[CEU][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs7308068	0.83[CEU][hapmap]
rs7315361	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7959802	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7972934	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9971666	0.88[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	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
rs10878397	HELB	cis	parietal	SCAN
rs10878397	HELB	cis	cerebellum	SCAN
rs10878397	HELB	Cis_1M	lymphoblastoid	RTeQTL
rs10878397	HELB	cis	Muscle Skeletal	GTEx

Chromatin state (count:14 , 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	chr12:66673800-66678200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:66674400-66678400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:66674600-66676800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr12:66674600-66677200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:66674800-66676600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr12:66674800-66677000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:66674800-66677200	Weak transcription	Primary T cells from cord blood	blood
9	chr12:66674800-66680000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:66675000-66676800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:66675000-66677000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr12:66675200-66677000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:66675200-66677200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:66675600-66680000	Weak transcription	Thymus	Thymus

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