Variant report

Variant	rs12061951
Chromosome Location	chr1:86081453-86081454
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:86046590..86049403-chr1:86080225..86081824,2	K562	blood:
2	chr1:86041810..86044112-chr1:86078850..86081561,2	K562	blood:
3	chr1:86040063..86041996-chr1:86079149..86082023,2	K562	blood:
4	chr1:86046852..86049403-chr1:86080324..86084474,3	K562	blood:

Variant related genes	Relation type
ENSG00000153904	Chromatin interaction
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10158408	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10493773	0.84[YRI][hapmap]
rs10493774	0.91[YRI][hapmap]
rs12066742	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12072027	0.86[CEU][hapmap]
rs12075929	0.81[ASW][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap]
rs12564080	0.92[LWK][hapmap]
rs12754358	0.84[YRI][hapmap]
rs1329961	0.81[CEU][hapmap]
rs17394091	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17398175	0.91[CEU][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17398321	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34746573	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3767163	0.84[YRI][hapmap]
rs7354850	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9651137	0.81[CEU][hapmap]
rs9803850	0.81[CEU][hapmap];0.84[MEX][hapmap];0.83[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1000290	chr1:86078495-86105379	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12061951	ZNHIT6	cis	lymphoblastoid	seeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86073200-86082200	Weak transcription	Aorta	Aorta
2	chr1:86077000-86083000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:86077800-86081800	Weak transcription	Right Atrium	heart
4	chr1:86078800-86081600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:86079000-86081800	Weak transcription	Ovary	ovary
6	chr1:86079000-86081800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:86079000-86082200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:86079200-86082400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:86079200-86085200	Weak transcription	Hela-S3	cervix
10	chr1:86079200-86086400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:86079200-86087800	Weak transcription	Left Ventricle	heart
12	chr1:86079200-86094400	Weak transcription	Pancreas	Pancrea
13	chr1:86079400-86081600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:86079400-86081800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:86079400-86082800	Weak transcription	A549	lung
16	chr1:86079400-86083000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:86079400-86084200	Enhancers	NHDF-Ad	bronchial
18	chr1:86079600-86082600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:86079600-86082600	Weak transcription	HSMMtube	muscle
20	chr1:86079600-86083000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:86079600-86083000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:86079600-86083000	Weak transcription	HSMM	muscle
23	chr1:86080200-86082000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:86080200-86082400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:86080200-86083000	Weak transcription	NHLF	lung
26	chr1:86080200-86083000	Weak transcription	Osteobl	bone
27	chr1:86080600-86082600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:86081000-86081600	Enhancers	Fetal Intestine Large	intestine
29	chr1:86081000-86081600	Enhancers	Fetal Intestine Small	intestine
30	chr1:86081000-86081600	Enhancers	NH-A	brain
31	chr1:86081000-86082200	Bivalent Enhancer	Fetal Brain Male	brain
32	chr1:86081200-86081600	Bivalent Enhancer	Brain Hippocampus Middle	brain
33	chr1:86081200-86081600	Enhancers	Fetal Brain Female	brain
34	chr1:86081200-86081800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:86081200-86081800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:86081200-86081800	Enhancers	Fetal Muscle Leg	muscle
37	chr1:86081200-86082000	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr1:86081200-86082200	Enhancers	Gastric	stomach
39	chr1:86081200-86082400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:86081200-86082400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr1:86081200-86083800	Enhancers	Placenta Amnion	Placenta Amnion
42	chr1:86081400-86081600	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr1:86081400-86081600	Active TSS	Brain Germinal Matrix	brain
44	chr1:86081400-86081600	Enhancers	Fetal Lung	lung
45	chr1:86081400-86081800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:86081400-86081800	Weak transcription	Placenta	Placenta
47	chr1:86081400-86082000	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr1:86081400-86082200	Enhancers	Fetal Heart	heart

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