Variant report

Variant	rs12757797
Chromosome Location	chr1:86088575-86088576
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	chr1:86045896..86049345-chr1:86088234..86091419,5	K562	blood:

Variant related genes	Relation type
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10873711	0.91[YRI][hapmap]
rs1360239	0.83[AFR][1000 genomes]
rs1481200	0.81[YRI][hapmap]
rs1764287	0.83[YRI][hapmap]
rs1764295	0.89[YRI][hapmap]
rs1775985	0.88[YRI][hapmap]
rs1775986	0.89[YRI][hapmap]
rs1775987	0.91[YRI][hapmap]
rs1775992	0.89[YRI][hapmap]
rs1999186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026772	0.86[YRI][hapmap]
rs2026773	0.80[CHB][hapmap];0.88[YRI][hapmap];0.82[ASN][1000 genomes]
rs2026774	0.83[YRI][hapmap]
rs2389973	0.81[YRI][hapmap]
rs399547	0.81[YRI][hapmap]
rs4949917	0.92[YRI][hapmap]
rs4949918	0.92[YRI][hapmap]
rs6576781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686719	0.81[YRI][hapmap]
rs6694808	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs7533395	0.88[YRI][hapmap]
rs821378	0.88[YRI][hapmap]
rs821380	0.89[YRI][hapmap]
rs821387	0.88[YRI][hapmap]
rs821388	0.84[YRI][hapmap]
rs821390	0.88[YRI][hapmap]
rs821400	0.87[YRI][hapmap]
rs821403	0.89[YRI][hapmap]
rs9324152	0.88[YRI][hapmap]
rs9661608	0.89[YRI][hapmap]
rs9661951	0.89[YRI][hapmap]
rs9701898	0.89[YRI][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	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
rs12757797	ZNHIT6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86079200-86094400	Weak transcription	Pancreas	Pancrea
2	chr1:86083800-86095200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:86083800-86103200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:86084600-86092800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:86085800-86093200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:86086200-86088600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:86086200-86088800	ZNF genes & repeats	Fetal Muscle Leg	muscle
8	chr1:86086400-86088600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
9	chr1:86086600-86088800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:86087200-86089800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:86087400-86088800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr1:86087400-86094400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:86087600-86088600	ZNF genes & repeats	HSMM	muscle
14	chr1:86087800-86088600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
15	chr1:86087800-86088600	ZNF genes & repeats	Left Ventricle	heart
16	chr1:86087800-86088800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
17	chr1:86087800-86088800	ZNF genes & repeats	Dnd41	blood
18	chr1:86087800-86089000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr1:86087800-86089400	Strong transcription	Primary B cells from cord blood	blood
20	chr1:86087800-86089400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:86088000-86088600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
22	chr1:86088000-86088600	ZNF genes & repeats	Psoas Muscle	Psoas
23	chr1:86088000-86088600	ZNF genes & repeats	Right Ventricle	heart
24	chr1:86088000-86088800	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr1:86088000-86089400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
26	chr1:86088000-86089400	ZNF genes & repeats	Primary T cells from cord blood	blood
27	chr1:86088000-86090400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:86088200-86088600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:86088200-86088600	ZNF genes & repeats	Thymus	Thymus
30	chr1:86088200-86088600	ZNF genes & repeats	A549	lung
31	chr1:86088200-86088800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:86088200-86088800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:86088200-86088800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:86088200-86088800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:86088200-86088800	ZNF genes & repeats	Liver	Liver
36	chr1:86088200-86089400	Enhancers	HSMMtube	muscle
37	chr1:86088200-86089400	Enhancers	NHDF-Ad	bronchial
38	chr1:86088200-86089400	Enhancers	NHLF	lung
39	chr1:86088200-86089400	Enhancers	Osteobl	bone
40	chr1:86088200-86089600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr1:86088200-86089600	Enhancers	NH-A	brain
42	chr1:86088200-86094400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:86088200-86101800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr1:86088400-86088600	ZNF genes & repeats	Fetal Intestine Large	intestine
45	chr1:86088400-86088600	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
46	chr1:86088400-86088600	ZNF genes & repeats	K562	blood
47	chr1:86088400-86088800	ZNF genes & repeats	Esophagus	oesophagus
48	chr1:86088400-86089000	ZNF genes & repeats	GM12878-XiMat	blood
49	chr1:86088400-86089200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:86088400-86089400	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell

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