Variant report

Variant	rs4709495
Chromosome Location	chr6:161550206-161550207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:161548242..161551323-chr6:161565381..161568765,4	K562	blood:
2	chr6:161548339..161550868-chr6:161560378..161562313,2	K562	blood:
3	chr6:161411333..161414575-chr6:161549147..161553015,4	K562	blood:
4	chr6:161547634..161549721-chr6:161550165..161554843,5	K562	blood:

Variant related genes	Relation type
ENSG00000085511	Chromatin interaction
ENSG00000272841	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1001809	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194157	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464779	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1464780	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1543261	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562026	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1982291	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2872613	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4472323	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4559074	1.00[ASN][1000 genomes]
rs4708898	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709486	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs4709489	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709490	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709491	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709492	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4709493	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709496	0.91[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587501	1.00[ASN][1000 genomes]
rs615269	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs619393	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs628430	1.00[ASN][1000 genomes]
rs628923	1.00[ASN][1000 genomes]
rs6455701	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6455703	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs645718	1.00[ASN][1000 genomes]
rs647923	0.84[TSI][hapmap]
rs657551	1.00[ASN][1000 genomes]
rs668638	1.00[ASN][1000 genomes]
rs682110	1.00[ASN][1000 genomes]
rs683549	1.00[ASN][1000 genomes]
rs6900500	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs6902332	1.00[ASN][1000 genomes]
rs6902760	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905942	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913706	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6918476	1.00[ASN][1000 genomes]
rs6919831	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923835	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs6925502	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6925800	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6929462	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6933810	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705829	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs705830	1.00[ASN][1000 genomes]
rs7738762	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7753585	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7760056	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9346846	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9355330	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9355332	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9355867	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9355872	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9355873	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9364585	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9364586	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9365248	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9458126	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030045	chr6:161359075-161562255	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1030852	chr6:161477750-161589394	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4709495	MAP3K4	cis	parietal	SCAN
rs4709495	MAS1	cis	cerebellum	SCAN
rs4709495	LOC729603	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161534600-161555800	Weak transcription	A549	lung
2	chr6:161534600-161559800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:161537600-161556800	Weak transcription	Gastric	stomach
4	chr6:161538200-161559600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:161538400-161553000	Weak transcription	Spleen	Spleen
6	chr6:161538400-161557800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:161538400-161558400	Weak transcription	HMEC	breast
8	chr6:161538600-161552600	Weak transcription	Pancreas	Pancrea
9	chr6:161538600-161554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:161538600-161555600	Weak transcription	NHLF	lung
11	chr6:161538600-161559600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:161538800-161553000	Weak transcription	Colonic Mucosa	Colon
13	chr6:161538800-161554400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:161539600-161550800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:161539800-161556800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr6:161539800-161557200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:161540600-161552800	Weak transcription	HUVEC	blood vessel
18	chr6:161541000-161584600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:161541400-161562200	Weak transcription	NHDF-Ad	bronchial
20	chr6:161542000-161567200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:161542000-161585600	Weak transcription	Fetal Kidney	kidney
22	chr6:161543800-161552200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
23	chr6:161543800-161554400	Weak transcription	Fetal Heart	heart
24	chr6:161544600-161555800	Weak transcription	Brain Angular Gyrus	brain
25	chr6:161544600-161589600	Weak transcription	Fetal Brain Male	brain
26	chr6:161544800-161553400	Weak transcription	Liver	Liver
27	chr6:161545000-161555400	Weak transcription	Psoas Muscle	Psoas
28	chr6:161545000-161555600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr6:161545000-161584800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:161545800-161551600	Weak transcription	HepG2	liver
31	chr6:161546200-161550400	Strong transcription	Primary hematopoietic stem cells	blood
32	chr6:161546200-161560800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:161546600-161555200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:161547400-161550600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:161547400-161551600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
36	chr6:161547400-161551800	Strong transcription	Left Ventricle	heart
37	chr6:161547400-161552000	Strong transcription	Thymus	Thymus
38	chr6:161547400-161554000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr6:161547600-161555600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr6:161547800-161550800	Weak transcription	Brain Substantia Nigra	brain
41	chr6:161547800-161550800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr6:161548000-161550400	Strong transcription	Esophagus	oesophagus
43	chr6:161548000-161551000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:161548000-161556200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:161548000-161557400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr6:161548200-161551400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr6:161548200-161556800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr6:161548200-161562000	Strong transcription	Fetal Intestine Small	intestine
49	chr6:161548200-161562800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:161548400-161550400	Weak transcription	Dnd41	blood

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