Variant report

Variant	rs9475837
Chromosome Location	chr6:57179847-57179848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr6:57179822-57180365	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56818167..56820292-chr6:57177596..57182762,4	MCF-7	breast:
2	chr6:57084710..57087719-chr6:57179458..57182091,4	MCF-7	breast:

Variant related genes	Relation type
PRIM2	TF binding region
ENSG00000112210	Chromatin interaction
ENSG00000151917	Chromatin interaction
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs12180921	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1741910	0.87[ASW][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1741911	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1741912	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1741913	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1741915	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1755831	1.00[ASN][1000 genomes]
rs1755834	0.87[ASW][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17705499	0.93[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs1888265	0.87[ASW][hapmap];0.88[GIH][hapmap]
rs1888266	0.87[ASW][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28367021	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28800513	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778513	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3778514	1.00[ASN][1000 genomes]
rs3800007	1.00[JPT][hapmap]
rs3800010	1.00[JPT][hapmap]
rs3800014	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3800016	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4615395	1.00[CEU][hapmap]
rs4712146	1.00[CEU][hapmap]
rs4715652	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4992408	1.00[CEU][hapmap]
rs58482037	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58651731	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59431929	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60821664	0.90[EUR][1000 genomes]
rs6459186	1.00[ASN][1000 genomes]
rs6459188	1.00[ASN][1000 genomes]
rs6911273	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911353	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936450	1.00[ASN][1000 genomes]
rs7754911	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9296875	1.00[JPT][hapmap]
rs9396273	1.00[ASN][1000 genomes]
rs9396274	0.89[ASN][1000 genomes]
rs9464433	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9464434	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464437	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464438	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464440	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs9475820	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475840	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475841	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475842	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9475844	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9475845	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475847	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475852	1.00[ASN][1000 genomes]
rs9475856	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475861	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9475862	0.87[ASN][1000 genomes]
rs9475863	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475882	1.00[JPT][hapmap]
rs9475887	1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9475837	HCRTR2	cis	parietal	SCAN
rs9475837	COL21A1	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:57176800-57181200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:57177000-57181200	Enhancers	NHDF-Ad	bronchial
3	chr6:57177600-57180000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:57177800-57180000	Enhancers	Fetal Stomach	stomach
5	chr6:57177800-57180400	Enhancers	HMEC	breast
6	chr6:57178200-57180000	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr6:57178600-57180200	Enhancers	HepG2	liver
8	chr6:57178600-57180400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr6:57178600-57180600	Enhancers	HSMMtube	muscle
10	chr6:57178600-57181200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:57178600-57181200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:57178600-57181200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr6:57178600-57181200	Enhancers	HSMM	muscle
14	chr6:57178600-57181200	Enhancers	Osteobl	bone
15	chr6:57178600-57181600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr6:57178800-57180200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:57178800-57180200	Enhancers	NH-A	brain
18	chr6:57178800-57180200	Enhancers	NHEK	skin
19	chr6:57178800-57180200	Enhancers	NHLF	lung
20	chr6:57178800-57181000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:57178800-57181200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:57178800-57181200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:57178800-57181200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr6:57178800-57181200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:57178800-57181200	Weak transcription	Stomach Mucosa	stomach
26	chr6:57178800-57181200	Weak transcription	K562	blood
27	chr6:57178800-57181400	Weak transcription	Fetal Intestine Small	intestine
28	chr6:57178800-57181400	Weak transcription	Ovary	ovary
29	chr6:57178800-57181400	Enhancers	Rectal Smooth Muscle	rectum
30	chr6:57178800-57181600	Weak transcription	Esophagus	oesophagus
31	chr6:57179000-57181200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:57179000-57181200	Weak transcription	Fetal Kidney	kidney
33	chr6:57179000-57181200	Weak transcription	Fetal Lung	lung
34	chr6:57179000-57181200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr6:57179200-57180200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:57179200-57181400	Weak transcription	Colonic Mucosa	Colon
37	chr6:57179200-57181400	Enhancers	Colon Smooth Muscle	Colon
38	chr6:57179200-57181600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:57179400-57181200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:57179400-57181200	Weak transcription	Fetal Muscle Leg	muscle
41	chr6:57179400-57181600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:57179600-57181200	Weak transcription	Hela-S3	cervix
43	chr6:57179800-57181000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:57179800-57181000	Weak transcription	HUVEC	blood vessel
45	chr6:57179800-57181200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:57179800-57181200	Weak transcription	A549	lung
47	chr6:57179800-57181400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:57179800-57181400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:57179800-57181400	Weak transcription	Aorta	Aorta

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