Variant report

Variant	rs6672838
Chromosome Location	chr1:92752308-92752309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr1:92752029-92752666	HepG2	liver:	n/a	chr1:92752543-92752558

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:92751701..92754444-chr1:92763776..92766491,2	MCF-7	breast:
2	chr1:92751144..92752872-chr1:92762540..92765121,2	K562	blood:

Variant related genes	Relation type
GLMN	TF binding region
ENSG00000174842	Chromatin interaction
ENSG00000122484	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10399671	1.00[EUR][1000 genomes]
rs11166542	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs12073894	1.00[CEU][hapmap]
rs12075168	1.00[EUR][1000 genomes]
rs12075243	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12098095	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17131621	1.00[CEU][hapmap]
rs17131632	1.00[EUR][1000 genomes]
rs17131636	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs41286805	0.87[EUR][1000 genomes]
rs41296171	0.87[EUR][1000 genomes]
rs41313389	0.87[EUR][1000 genomes]
rs55993081	1.00[EUR][1000 genomes]
rs56297403	0.87[EUR][1000 genomes]
rs57177520	0.87[EUR][1000 genomes]
rs57217458	0.87[EUR][1000 genomes]
rs58142139	0.87[EUR][1000 genomes]
rs59278612	0.87[EUR][1000 genomes]
rs60265386	0.87[EUR][1000 genomes]
rs60550001	0.87[EUR][1000 genomes]
rs60755573	0.87[EUR][1000 genomes]
rs60933677	0.87[EUR][1000 genomes]
rs61141829	0.87[EUR][1000 genomes]
rs61185080	0.87[EUR][1000 genomes]
rs61410146	0.87[EUR][1000 genomes]
rs6660858	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6661028	0.87[EUR][1000 genomes]
rs6662565	1.00[CEU][hapmap]
rs6681027	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs6681213	0.87[EUR][1000 genomes]
rs6683456	1.00[EUR][1000 genomes]
rs6695475	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6702975	0.87[EUR][1000 genomes]
rs6704484	0.87[EUR][1000 genomes]
rs72958740	0.87[EUR][1000 genomes]
rs72958746	0.87[EUR][1000 genomes]
rs72958774	0.87[EUR][1000 genomes]
rs72958781	0.87[EUR][1000 genomes]
rs72958796	0.87[EUR][1000 genomes]
rs72960815	0.87[EUR][1000 genomes]
rs72960831	0.87[EUR][1000 genomes]
rs72960835	0.87[EUR][1000 genomes]
rs72960847	0.87[EUR][1000 genomes]
rs72960860	0.87[EUR][1000 genomes]
rs72960870	0.87[EUR][1000 genomes]
rs72960872	1.00[EUR][1000 genomes]
rs72962640	0.87[EUR][1000 genomes]
rs72962659	1.00[EUR][1000 genomes]
rs74101123	0.87[EUR][1000 genomes]
rs74101131	0.87[EUR][1000 genomes]
rs74101133	0.87[EUR][1000 genomes]
rs74101146	0.87[EUR][1000 genomes]
rs74101152	0.87[EUR][1000 genomes]
rs74101157	0.87[EUR][1000 genomes]
rs74102832	0.87[EUR][1000 genomes]
rs74102844	0.87[EUR][1000 genomes]
rs74102853	0.87[EUR][1000 genomes]
rs74102861	0.87[EUR][1000 genomes]
rs7513631	0.87[EUR][1000 genomes]
rs7519603	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7520555	1.00[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs7520675	1.00[EUR][1000 genomes]
rs7525174	0.87[EUR][1000 genomes]
rs7527960	1.00[EUR][1000 genomes]
rs7529971	1.00[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs7534750	0.87[EUR][1000 genomes]
rs7535181	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs7542362	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7542736	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv871508	chr1:92478130-92781579	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv830592	chr1:92669282-92805629	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv870667	chr1:92697188-92813741	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92707200-92764000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:92709000-92762800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:92710600-92753200	Weak transcription	Small Intestine	intestine
4	chr1:92710600-92762000	Weak transcription	Fetal Brain Male	brain
5	chr1:92710600-92763400	Weak transcription	Brain Angular Gyrus	brain
6	chr1:92710600-92764000	Weak transcription	Gastric	stomach
7	chr1:92711000-92763600	Weak transcription	HSMMtube	muscle
8	chr1:92711200-92761600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:92711200-92764000	Weak transcription	Spleen	Spleen
10	chr1:92719400-92764000	Weak transcription	Pancreas	Pancrea
11	chr1:92719600-92760800	Weak transcription	Fetal Heart	heart
12	chr1:92720000-92763800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:92722400-92763400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:92723000-92763800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:92724000-92760600	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:92724600-92763800	Weak transcription	Brain Substantia Nigra	brain
17	chr1:92725800-92764000	Weak transcription	Colonic Mucosa	Colon
18	chr1:92727000-92763800	Weak transcription	Right Ventricle	heart
19	chr1:92727200-92759200	Weak transcription	A549	lung
20	chr1:92727200-92763800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:92729800-92763800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:92732000-92763600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:92733600-92754800	Weak transcription	HMEC	breast
24	chr1:92735200-92752400	Weak transcription	Psoas Muscle	Psoas
25	chr1:92736000-92763600	Weak transcription	Liver	Liver
26	chr1:92736800-92763800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:92737800-92759400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:92738000-92760600	Weak transcription	Hela-S3	cervix
29	chr1:92738000-92763800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:92738400-92763800	Weak transcription	Brain Anterior Caudate	brain
31	chr1:92738800-92763400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr1:92740800-92752400	Weak transcription	HSMM	muscle
33	chr1:92741000-92754400	Weak transcription	K562	blood
34	chr1:92741400-92754000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:92742200-92754600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:92742400-92753600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:92743200-92753600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:92743200-92759200	Weak transcription	NHLF	lung
39	chr1:92743200-92759600	Weak transcription	Osteobl	bone
40	chr1:92743200-92763600	Weak transcription	NHDF-Ad	bronchial
41	chr1:92743400-92752400	Weak transcription	NH-A	brain
42	chr1:92743800-92754000	Weak transcription	Primary B cells from cord blood	blood
43	chr1:92743800-92754400	Weak transcription	HepG2	liver
44	chr1:92744000-92764000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:92745600-92764000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:92745800-92753400	Weak transcription	Placenta	Placenta
47	chr1:92745800-92753600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:92745800-92753800	Weak transcription	Brain Germinal Matrix	brain
49	chr1:92745800-92754000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr1:92745800-92754800	Weak transcription	Brain Hippocampus Middle	brain

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