Variant report

Variant	rs6932585
Chromosome Location	chr6:119143549-119143550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1022707	0.94[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap]
rs1022708	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs11153782	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1885125	0.95[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap]
rs2145569	0.95[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap]
rs284919	0.90[JPT][hapmap]
rs4027592	0.98[ASN][1000 genomes]
rs4946365	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4946367	0.81[ASN][1000 genomes]
rs4946372	0.95[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap]
rs4946373	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4946382	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs6904381	0.95[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap]
rs6918844	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6929403	0.85[CHB][hapmap]
rs6931423	0.81[ASN][1000 genomes]
rs6939937	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7381535	0.95[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs7743045	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs9320671	0.95[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.90[TSI][hapmap]
rs9374754	0.85[EUR][1000 genomes]
rs9387621	0.95[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap]
rs9387624	0.85[CHB][hapmap]
rs9401106	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs988098	0.81[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]

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	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1020405	chr6:118786586-119241006	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv830788	chr6:119014021-119143652	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1023826	chr6:119026481-119221408	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6932585	MCM9	cis	cerebellum	SCAN
rs6932585	MCMDC1	cis	multi-tissue	Pritchard
rs6932585	FAM184A	cis	parietal	SCAN
rs6932585	MCM9	cis	lymphoblastoid	seeQTL
rs6932585	TSPYL1	cis	cerebellum	SCAN
rs6932585	MCM9	cis	Lymphoblastoid	GTEx
rs6932585	MCM9	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119122000-119147000	Weak transcription	Stomach Mucosa	stomach
2	chr6:119122200-119147000	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:119122400-119146800	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:119122600-119144000	Weak transcription	Brain Angular Gyrus	brain
5	chr6:119125600-119143600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:119128600-119151600	Weak transcription	Colonic Mucosa	Colon
7	chr6:119130600-119146400	Weak transcription	Psoas Muscle	Psoas
8	chr6:119132200-119143600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:119132200-119145400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:119132200-119146400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr6:119132200-119150600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:119132400-119146800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr6:119132400-119150800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr6:119133400-119148000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:119133400-119151800	Weak transcription	Fetal Kidney	kidney
16	chr6:119134000-119150600	Weak transcription	Hela-S3	cervix
17	chr6:119134200-119143600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:119134200-119143600	Weak transcription	HUVEC	blood vessel
19	chr6:119134200-119144000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:119134400-119143600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:119134400-119146600	Weak transcription	Brain Anterior Caudate	brain
22	chr6:119134400-119146800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr6:119134400-119147000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:119134400-119147000	Weak transcription	Small Intestine	intestine
25	chr6:119135000-119146600	Weak transcription	GM12878-XiMat	blood
26	chr6:119135200-119150600	Weak transcription	NHLF	lung
27	chr6:119135400-119146600	Weak transcription	HMEC	breast
28	chr6:119135400-119146600	Weak transcription	NHEK	skin
29	chr6:119135400-119146600	Weak transcription	Osteobl	bone
30	chr6:119135400-119149000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:119135400-119150200	Weak transcription	Brain Substantia Nigra	brain
32	chr6:119135400-119151000	Weak transcription	NH-A	brain
33	chr6:119135400-119151400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr6:119135600-119146200	Weak transcription	HSMM	muscle
35	chr6:119135800-119146200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:119135800-119151000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:119136800-119143600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr6:119137000-119144000	Weak transcription	Brain Germinal Matrix	brain
39	chr6:119137200-119143600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:119137200-119143600	Weak transcription	Lung	lung
41	chr6:119137200-119143600	Weak transcription	Thymus	Thymus
42	chr6:119137200-119145800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:119137200-119146600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr6:119137200-119146800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr6:119137200-119149000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr6:119137400-119143600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:119137400-119143600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:119137400-119143600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:119137400-119143600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr6:119137400-119143600	Weak transcription	Fetal Stomach	stomach

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