Variant report

Variant	rs2096284
Chromosome Location	chr6:140069122-140069123
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:139695575..139697248-chr6:140068689..140071855,3	MCF-7	breast:
2	chr6:140067390..140069784-chr6:140078728..140080406,2	K562	blood:
3	chr6:140068204..140070136-chr6:140072502..140075206,2	K562	blood:
4	chr6:140062822..140064897-chr6:140067790..140070616,2	K562	blood:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10499213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10499214	0.99[ASN][1000 genomes]
rs11962730	0.86[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];0.97[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11963532	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964275	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.99[ASN][1000 genomes]
rs12055436	0.93[ASW][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.81[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12055472	0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs12055843	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12662206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17069206	0.88[JPT][hapmap]
rs17069225	0.93[ASW][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];0.81[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1891808	0.86[AFR][1000 genomes]
rs1936210	0.89[ASN][1000 genomes]
rs1936214	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2096283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154032	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2185923	0.88[ASN][1000 genomes]
rs2327993	0.88[ASN][1000 genomes]
rs4520026	0.99[ASN][1000 genomes]
rs4535566	0.86[ASN][1000 genomes]
rs55764205	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs55966840	0.99[ASN][1000 genomes]
rs60350063	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60758082	0.88[ASN][1000 genomes]
rs6570372	0.89[ASN][1000 genomes]
rs6570373	0.90[ASN][1000 genomes]
rs6570374	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6901783	0.94[JPT][hapmap]
rs6905478	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6933318	0.94[JPT][hapmap]
rs73556090	0.88[ASN][1000 genomes]
rs73558032	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743796	0.99[ASN][1000 genomes]
rs7752001	0.88[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7752323	0.89[ASN][1000 genomes]
rs7756866	0.99[ASN][1000 genomes]
rs7769567	0.97[ASN][1000 genomes]
rs7774968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9321752	0.88[ASN][1000 genomes]
rs9373246	0.82[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs9373247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376452	0.87[ASW][hapmap];0.80[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs9376457	0.89[ASN][1000 genomes]
rs9376466	0.81[EUR][1000 genomes]
rs9385874	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9385875	0.99[ASN][1000 genomes]
rs9385876	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9389715	0.89[ASN][1000 genomes]
rs9389717	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9399292	0.88[JPT][hapmap]
rs9403113	0.88[ASN][1000 genomes]
rs9403114	0.99[ASN][1000 genomes]
rs9403115	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9403116	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[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	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv464065	chr6:140027836-140085873	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv604766	chr6:140027836-140085873	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2096284	MAP3K5	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140054800-140072000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:140064400-140070000	Enhancers	Fetal Intestine Large	intestine
3	chr6:140064800-140069200	Weak transcription	HSMMtube	muscle
4	chr6:140065400-140069200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:140065400-140069400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:140065400-140069400	Weak transcription	Hela-S3	cervix
7	chr6:140065400-140069600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:140065400-140071800	Weak transcription	HepG2	liver
9	chr6:140065600-140069600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:140065600-140069800	Weak transcription	NHEK	skin
11	chr6:140066000-140073400	Weak transcription	HSMM	muscle
12	chr6:140066200-140069200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:140066200-140072800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:140066400-140069200	Weak transcription	NHLF	lung
15	chr6:140066400-140069600	Weak transcription	NH-A	brain
16	chr6:140066400-140069800	Weak transcription	Fetal Kidney	kidney
17	chr6:140066400-140072200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:140066400-140074800	Weak transcription	A549	lung
19	chr6:140066600-140071800	Weak transcription	NHDF-Ad	bronchial
20	chr6:140066800-140073400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:140067400-140069400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:140067600-140069200	Weak transcription	Osteobl	bone
23	chr6:140067800-140070400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr6:140067800-140070600	Enhancers	Fetal Intestine Small	intestine
25	chr6:140068200-140070200	Enhancers	Ovary	ovary
26	chr6:140068200-140070800	Enhancers	Placenta Amnion	Placenta Amnion
27	chr6:140068400-140069600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:140068400-140070200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:140068400-140070200	Enhancers	Placenta	Placenta
30	chr6:140068400-140070200	Enhancers	Right Atrium	heart
31	chr6:140068800-140070400	Enhancers	Adipose Nuclei	Adipose
32	chr6:140069000-140069200	Enhancers	Pancreas	Pancrea
33	chr6:140069000-140070200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:140069000-140070200	Enhancers	Fetal Lung	lung
35	chr6:140069000-140071000	Enhancers	Fetal Heart	heart

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