Variant report

Variant	rs6905478
Chromosome Location	chr6:140076028-140076029
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:139694150..139697006-chr6:140073996..140076840,3	MCF-7	breast:
2	chr6:140073591..140076485-chr6:140078256..140081113,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10499213	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10499214	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11962730	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11963532	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11964275	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11965819	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12055436	0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs12055472	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs12055843	0.88[ASN][1000 genomes]
rs12662206	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12664473	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17069206	0.82[JPT][hapmap]
rs17069225	0.88[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs1936210	0.90[ASN][1000 genomes]
rs1936214	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2096283	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2096284	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]
rs2154032	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185923	0.89[ASN][1000 genomes]
rs2327993	0.89[ASN][1000 genomes]
rs4520026	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535566	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4896488	0.84[AMR][1000 genomes]
rs55764205	0.88[ASN][1000 genomes]
rs55966840	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60052799	0.84[AMR][1000 genomes]
rs60350063	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs60758082	0.88[ASN][1000 genomes]
rs60870127	0.80[ASN][1000 genomes]
rs6570372	0.90[ASN][1000 genomes]
rs6570373	0.89[ASN][1000 genomes]
rs6570374	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6901783	0.94[CEU][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6911905	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6933318	0.94[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6933569	0.84[AMR][1000 genomes]
rs73556090	0.89[ASN][1000 genomes]
rs73558032	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73775693	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7743796	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752001	0.88[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs7752323	0.90[ASN][1000 genomes]
rs7756866	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769567	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7772473	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7774968	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776193	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9321752	0.87[ASN][1000 genomes]
rs9373246	0.82[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs9373247	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9373248	1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9376452	0.80[GIH][hapmap];0.82[JPT][hapmap]
rs9376457	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9385874	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9385875	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9385876	0.94[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs9389715	0.90[ASN][1000 genomes]
rs9389717	0.88[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9399292	0.82[JPT][hapmap]
rs9399293	0.83[AMR][1000 genomes]
rs9403113	0.89[ASN][1000 genomes]
rs9403114	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403115	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403116	0.94[CHB][hapmap];0.93[JPT][hapmap];0.98[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
rs6905478	MAP3K5	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140070200-140085200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:140071800-140077000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:140071800-140079200	Enhancers	Osteobl	bone
4	chr6:140072200-140077400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:140072400-140079200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:140073000-140089400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:140073400-140076800	Enhancers	HSMM	muscle
8	chr6:140073400-140079200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr6:140073600-140076800	Enhancers	HSMMtube	muscle
10	chr6:140073800-140076800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:140074000-140079400	Weak transcription	Aorta	Aorta
12	chr6:140074400-140077000	Enhancers	Fetal Kidney	kidney
13	chr6:140074400-140078600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:140074600-140076200	Enhancers	Placenta Amnion	Placenta Amnion
15	chr6:140074600-140076200	Enhancers	HepG2	liver
16	chr6:140074600-140076800	Enhancers	Fetal Heart	heart
17	chr6:140074600-140076800	Enhancers	Fetal Lung	lung
18	chr6:140074800-140076400	Enhancers	A549	lung
19	chr6:140074800-140078200	Weak transcription	Psoas Muscle	Psoas
20	chr6:140075000-140076200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:140075000-140076200	Weak transcription	HUVEC	blood vessel
22	chr6:140075000-140076800	Enhancers	NHLF	lung
23	chr6:140075000-140083200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:140075000-140085400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr6:140075200-140083800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:140075600-140081200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:140075800-140076400	Enhancers	Fetal Muscle Leg	muscle
28	chr6:140075800-140076400	Enhancers	Right Atrium	heart
29	chr6:140075800-140076800	Enhancers	Small Intestine	intestine
30	chr6:140075800-140077200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:140075800-140077400	Enhancers	Fetal Intestine Small	intestine
32	chr6:140075800-140077400	Enhancers	Ovary	ovary
33	chr6:140075800-140077400	Enhancers	Pancreas	Pancrea
34	chr6:140075800-140077600	Enhancers	Adipose Nuclei	Adipose
35	chr6:140075800-140077600	Enhancers	Fetal Intestine Large	intestine
36	chr6:140076000-140076200	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr6:140076000-140076400	Enhancers	Right Ventricle	heart
38	chr6:140076000-140076400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr6:140076000-140076400	Enhancers	Stomach Smooth Muscle	stomach
40	chr6:140076000-140076400	Enhancers	Hela-S3	cervix
41	chr6:140076000-140076400	Flanking Active TSS	NHDF-Ad	bronchial
42	chr6:140076000-140076600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:140076000-140076800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:140076000-140076800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:140076000-140076800	Flanking Active TSS	Liver	Liver
46	chr6:140076000-140076800	Enhancers	Duodenum Mucosa	Duodenum
47	chr6:140076000-140076800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr6:140076000-140076800	Enhancers	Fetal Stomach	stomach
49	chr6:140076000-140076800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr6:140076000-140077000	Enhancers	Pancreatic Islets	Pancreatic Islet

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