Variant report

Variant	rs3812475
Chromosome Location	chr8:125463250-125463251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:125460680..125466261-chr8:125549985..125555147,10	K562	blood:
2	chr8:125459763..125466513-chr8:125482159..125488968,22	K562	blood:
3	chr8:125459763..125466594-chr8:125480347..125488760,16	K562	blood:
4	chr2:231280254..231281169-chr8:125462695..125463364,2	NB4	blood:
5	chr14:24609134..24611550-chr8:125461758..125464369,2	MCF-7	breast:
6	chr12:7072260..7073970-chr8:125462442..125465411,2	MCF-7	breast:
7	chr8:125461877..125466400-chr8:125548792..125551961,4	MCF-7	breast:
8	chr8:125463239..125464155-chr8:125486423..125486982,2	MCF-7	breast:
9	chr8:125461480..125466921-chr8:125547850..125552862,10	MCF-7	breast:
10	chr8:125458285..125469406-chr8:125482519..125490004,41	MCF-7	breast:
11	chr8:125459427..125466261-chr8:125549985..125555147,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000170881	Chromatin interaction
ENSG00000207713	Chromatin interaction
ENSG00000067066	Chromatin interaction
ENSG00000147684	Chromatin interaction
ENSG00000207708	Chromatin interaction
ENSG00000126749	Chromatin interaction
ENSG00000100908	Chromatin interaction
ENSG00000257084	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000245149	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10091243	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10092569	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10106292	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11987932	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11991829	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12542293	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12548235	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28725399	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3812471	0.87[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3812472	0.87[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3812474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3886003	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4128468	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4132855	0.92[MEX][hapmap];0.80[AMR][1000 genomes]
rs4269525	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4269526	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4871498	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6470243	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6470245	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6982197	0.92[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[EUR][1000 genomes]
rs6984985	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6987343	0.92[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs6993926	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7001480	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7005393	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7007115	0.92[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs7009290	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7010411	0.90[JPT][hapmap]
rs7013683	0.80[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7812331	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7812363	0.80[AMR][1000 genomes]
rs7812911	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7825599	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7827791	0.92[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7830506	0.87[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762769	chr8:125167256-125480574	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1034768	chr8:125323011-125481733	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv891430	chr8:125431030-125485027	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1017848	chr8:125432689-125489052	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
6	nsv891431	chr8:125437811-125485027	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv891432	chr8:125438093-125485027	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv891433	chr8:125438093-125498547	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3812475	ZHX2	cis	parietal	SCAN
rs3812475	TRMT12	cis	uninvolved skin	skin_eQTL
rs3812475	TRMT12	cis	Whole Blood	GTEx
rs3812475	TRMT12	Cis_1M	lymphoblastoid	RTeQTL
rs3812475	TRMT12	cis	lymphoblastoid	seeQTL
rs3812475	TRMT12	cis	multi-tissue	Pritchard
rs3812475	ENSG00000183665	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125462000-125463400	Active TSS	Rectal Smooth Muscle	rectum
2	chr8:125462000-125463400	Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr8:125462000-125463600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr8:125462000-125463600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr8:125462000-125463600	Active TSS	Brain Anterior Caudate	brain
6	chr8:125462000-125463600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr8:125462000-125463600	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr8:125462000-125463600	Active TSS	Fetal Lung	lung
9	chr8:125462000-125463600	Active TSS	Ovary	ovary
10	chr8:125462000-125463600	Active TSS	Right Atrium	heart
11	chr8:125462000-125463800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr8:125462000-125463800	Active TSS	Aorta	Aorta
13	chr8:125462000-125463800	Active TSS	Colon Smooth Muscle	Colon
14	chr8:125462000-125464000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr8:125462000-125464200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr8:125462000-125464200	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr8:125462000-125464600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr8:125462200-125463400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr8:125462200-125463400	Active TSS	Brain Angular Gyrus	brain
20	chr8:125462200-125463400	Active TSS	Duodenum Mucosa	Duodenum
21	chr8:125462200-125463400	Active TSS	Fetal Muscle Trunk	muscle
22	chr8:125462200-125463400	Active TSS	Pancreas	Pancrea
23	chr8:125462200-125463600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr8:125462200-125463600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr8:125462200-125463600	Active TSS	Brain Cingulate Gyrus	brain
26	chr8:125462200-125463600	Active TSS	Brain Substantia Nigra	brain
27	chr8:125462200-125463600	Active TSS	Esophagus	oesophagus
28	chr8:125462200-125463600	Active TSS	Fetal Intestine Small	intestine
29	chr8:125462200-125463600	Active TSS	Fetal Stomach	stomach
30	chr8:125462200-125463600	Active TSS	Left Ventricle	heart
31	chr8:125462200-125463600	Active TSS	Stomach Smooth Muscle	stomach
32	chr8:125462200-125463600	Active TSS	NH-A	brain
33	chr8:125462200-125463800	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr8:125462200-125463800	Active TSS	Fetal Intestine Large	intestine
35	chr8:125462200-125463800	Active TSS	Fetal Kidney	kidney
36	chr8:125462200-125463800	Active TSS	Psoas Muscle	Psoas
37	chr8:125462200-125463800	Active TSS	Right Ventricle	heart
38	chr8:125462200-125463800	Active TSS	A549	lung
39	chr8:125462200-125463800	Active TSS	GM12878-XiMat	blood
40	chr8:125462200-125463800	Active TSS	HSMMtube	muscle
41	chr8:125462200-125463800	Active TSS	NHLF	lung
42	chr8:125462200-125464000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr8:125462200-125464200	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr8:125462200-125464200	Flanking Active TSS	Liver	Liver
45	chr8:125462200-125464200	Active TSS	Colonic Mucosa	Colon
46	chr8:125462400-125463400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr8:125462400-125463400	Active TSS	Brain Germinal Matrix	brain
48	chr8:125462400-125463400	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr8:125462400-125463400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr8:125462400-125463400	Active TSS	Fetal Brain Female	brain

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