Variant report

Variant	rs2007339
Chromosome Location	chr6:131345664-131345665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:131341511..131345249-chr6:131345439..131348645,4	K562	blood:
2	chr6:131345332..131348195-chr6:131348850..131352317,3	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1043598	0.93[CHD][hapmap];0.92[JPT][hapmap]
rs10499174	0.92[JPT][hapmap]
rs12661081	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12664355	0.93[CHD][hapmap];0.92[JPT][hapmap]
rs12965	0.93[CHD][hapmap];0.92[JPT][hapmap]
rs13193246	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1332490	0.89[CEU][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1332491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1338905	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17059681	0.93[CHD][hapmap];0.92[JPT][hapmap]
rs17059683	0.92[JPT][hapmap]
rs17059698	0.92[JPT][hapmap]
rs17059702	0.92[JPT][hapmap]
rs17059896	0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs17059925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17831009	0.92[JPT][hapmap]
rs1855077	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1888959	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1976982	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2151069	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2225557	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2275063	0.92[JPT][hapmap]
rs2275065	0.81[ASN][1000 genomes]
rs3777450	0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs3777453	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs3777463	0.88[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs3822864	0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs4895902	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4897480	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897481	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897482	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897488	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4897490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56027377	0.81[ASN][1000 genomes]
rs6569716	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6569718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6569722	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6569725	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6900810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908917	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6909134	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6928986	0.89[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6942081	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73623428	0.99[ASN][1000 genomes]
rs73774307	0.81[ASN][1000 genomes]
rs73774328	0.91[ASN][1000 genomes]
rs7742376	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7747881	0.88[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs7765007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7765757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769153	0.88[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs9321268	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9372988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9689026	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2007339	ARG1	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131329800-131347400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:131337400-131347200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:131337800-131351000	Weak transcription	Stomach Mucosa	stomach
4	chr6:131339400-131349400	Weak transcription	Brain Angular Gyrus	brain
5	chr6:131344400-131347600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:131345000-131345800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:131345000-131345800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr6:131345000-131345800	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr6:131345000-131345800	Enhancers	HSMM	muscle
10	chr6:131345000-131345800	Enhancers	HSMMtube	muscle
11	chr6:131345000-131345800	Flanking Active TSS	NHEK	skin
12	chr6:131345000-131346000	Enhancers	A549	lung
13	chr6:131345000-131346000	Enhancers	HUVEC	blood vessel
14	chr6:131345000-131346000	Enhancers	Osteobl	bone
15	chr6:131345000-131347000	Enhancers	NHLF	lung
16	chr6:131345000-131348000	Enhancers	Brain Anterior Caudate	brain
17	chr6:131345000-131348800	Enhancers	Brain Hippocampus Middle	brain
18	chr6:131345200-131345800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr6:131345200-131345800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:131345200-131345800	Enhancers	Brain Cingulate Gyrus	brain
21	chr6:131345200-131345800	Enhancers	Fetal Muscle Leg	muscle
22	chr6:131345200-131345800	Enhancers	Ovary	ovary
23	chr6:131345200-131345800	Enhancers	Small Intestine	intestine
24	chr6:131345200-131346000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:131345200-131346000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:131345200-131346000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:131345200-131346000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:131345200-131346000	Enhancers	Colon Smooth Muscle	Colon
29	chr6:131345200-131346000	Enhancers	HepG2	liver
30	chr6:131345200-131346000	Enhancers	NH-A	brain
31	chr6:131345200-131346200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:131345200-131348000	Enhancers	Brain Substantia Nigra	brain
33	chr6:131345400-131345800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:131345400-131345800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:131345400-131345800	Enhancers	Left Ventricle	heart
36	chr6:131345400-131345800	Enhancers	Lung	lung
37	chr6:131345400-131345800	Enhancers	Right Atrium	heart
38	chr6:131345400-131346200	Enhancers	GM12878-XiMat	blood
39	chr6:131345400-131347000	Enhancers	Hela-S3	cervix
40	chr6:131345600-131345800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:131345600-131345800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:131345600-131345800	Enhancers	Primary hematopoietic stem cells	blood
43	chr6:131345600-131345800	Enhancers	Duodenum Mucosa	Duodenum
44	chr6:131345600-131346000	Enhancers	HMEC	breast
45	chr6:131345600-131346600	Weak transcription	Adipose Nuclei	Adipose
46	chr6:131345600-131346800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr6:131345600-131347200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:131345600-131347600	Enhancers	NHDF-Ad	bronchial
49	chr6:131345600-131350400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:131345600-131350600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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