Variant report

Variant	rs3780087
Chromosome Location	chr8:6568201-6568202
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	POLR2A	chr8:6563393-6568475	GM18505	blood:	n/a	n/a
2	PML	chr8:6564863-6568603	GM12878	blood:	n/a	n/a
3	POLR2A	chr8:6564875-6568226	GM12892	blood:	n/a	n/a
4	MTA3	chr8:6566084-6568380	GM12878	blood:	n/a	n/a
5	BCLAF1	chr8:6565082-6568240	GM12878	blood:	n/a	chr8:6565887-6565900 chr8:6566647-6566660 chr8:6566634-6566643 chr8:6565982-6565995
6	POLR2A	chr8:6563528-6568801	GM12878	blood:	n/a	n/a
7	POLR2A	chr8:6568089-6568358	MCF10A-Er-Src	breast:	n/a	n/a
8	CHD1	chr8:6565011-6568398	GM12878	blood:	n/a	chr8:6566145-6566155
9	MYC	chr8:6567768-6568297	MCF10A-Er-Src	breast:	n/a	n/a
10	IRF1	chr8:6567855-6568285	K562	blood:	n/a	n/a
11	NFATC1	chr8:6567043-6568536	GM12878	blood:	n/a	n/a
12	POLR2A	chr8:6563320-6569676	GM12878	blood:	n/a	n/a
13	POLR2A	chr8:6563304-6568497	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:6285374..6287527-chr8:6566715..6569546,2	K562	blood:
2	chr8:6263912..6265972-chr8:6565205..6568456,4	K562	blood:
3	chr8:6567182..6570049-chr8:6639193..6642155,2	K562	blood:
4	chr8:6567796..6570649-chr8:6571999..6573620,2	MCF-7	breast:
5	chr8:6566127..6567719-chr8:6567904..6569806,2	MCF-7	breast:
6	chr8:6566710..6569259-chr8:6614504..6616089,2	K562	blood:
7	chr8:6566568..6569324-chr8:6619809..6622501,2	K562	blood:
8	chr8:6564149..6568457-chr8:6601682..6605924,8	K562	blood:
9	chr8:6567971..6570094-chr8:6598474..6600229,2	MCF-7	breast:
10	chr11:62607824..62609645-chr8:6566131..6568713,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249898	TF binding region
ENSG00000266038	Chromatin interaction
ENSG00000155189	Chromatin interaction
ENSG00000246089	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000147316	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10096753	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10108451	0.85[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10110103	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs11986408	0.90[ASN][1000 genomes]
rs11986409	0.90[ASN][1000 genomes]
rs11996255	0.90[ASN][1000 genomes]
rs11996256	0.90[ASN][1000 genomes]
rs1365042	0.92[CEU][hapmap];0.98[GIH][hapmap];0.85[YRI][hapmap]
rs1559744	0.96[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1559748	0.92[CEU][hapmap]
rs1961768	0.82[EUR][1000 genomes]
rs1971312	0.92[CEU][hapmap]
rs2408444	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28476773	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2911975	0.92[CEU][hapmap]
rs2911976	0.92[CEU][hapmap];0.89[GIH][hapmap]
rs2911977	0.92[CEU][hapmap];0.89[GIH][hapmap]
rs2911978	0.92[CEU][hapmap]
rs2911979	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2911980	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2911982	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2911983	0.98[ASN][1000 genomes]
rs2912054	0.84[CEU][hapmap];0.87[GIH][hapmap]
rs2912067	0.85[EUR][1000 genomes]
rs2928576	0.85[CEU][hapmap]
rs2928623	0.92[CEU][hapmap];0.89[GIH][hapmap]
rs2928625	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2928626	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs2928629	0.92[CEU][hapmap];0.89[GIH][hapmap]
rs2928630	0.92[CEU][hapmap]
rs2936502	0.85[CEU][hapmap]
rs2936512	0.81[CEU][hapmap]
rs2936520	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs2980679	0.81[CEU][hapmap]
rs2980680	0.88[CEU][hapmap]
rs2980683	0.92[CEU][hapmap];0.89[GIH][hapmap]
rs2980684	0.92[CEU][hapmap];0.89[GIH][hapmap]
rs2980686	0.85[GIH][hapmap]
rs2980689	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2980690	0.92[CEU][hapmap];0.83[YRI][hapmap]
rs6559177	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6559178	0.86[CEU][hapmap]
rs992812	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs992813	0.85[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1015981	chr8:6286575-6578450	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1027313	chr8:6286575-6920312	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1021684	chr8:6350091-6809455	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	esv2422383	chr8:6362389-6781593	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv610004	chr8:6402366-6772913	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1029241	chr8:6411300-6761720	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv933075	chr8:6456475-7366650	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
10	nsv1025976	chr8:6472948-6686972	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv933768	chr8:6482944-6618221	Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv831220	chr8:6527845-6728491	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	nsv1030637	chr8:6545498-6669949	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
14	nsv1034115	chr8:6546984-6665832	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
15	nsv465436	chr8:6568201-6921404	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv610006	chr8:6568201-6921404	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3780087	MMGT1	trans	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6564000-6568400	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr8:6564600-6568800	Active TSS	GM12878-XiMat	blood
3	chr8:6564800-6568600	Active TSS	K562	blood
4	chr8:6566400-6568400	Flanking Active TSS	HUVEC	blood vessel
5	chr8:6566600-6568400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr8:6566600-6568400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr8:6566600-6568400	Active TSS	Brain Germinal Matrix	brain
8	chr8:6566800-6575800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr8:6566800-6575800	Weak transcription	Spleen	Spleen
10	chr8:6567000-6569200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr8:6567000-6569200	Weak transcription	Esophagus	oesophagus
12	chr8:6567000-6569200	Weak transcription	Lung	lung
13	chr8:6567000-6571000	Weak transcription	Small Intestine	intestine
14	chr8:6567000-6575600	Weak transcription	Gastric	stomach
15	chr8:6567000-6578000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr8:6567000-6580200	Weak transcription	Right Ventricle	heart
17	chr8:6567200-6568400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr8:6567200-6569600	Transcr. at gene 5' and 3'	Dnd41	blood
19	chr8:6567400-6568400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr8:6567400-6569000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr8:6567400-6571000	Weak transcription	Brain Anterior Caudate	brain
22	chr8:6567400-6575600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr8:6567400-6578000	Weak transcription	Brain Angular Gyrus	brain
24	chr8:6567400-6586800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr8:6567400-6590000	Weak transcription	Left Ventricle	heart
26	chr8:6567400-6590200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr8:6567400-6590600	Weak transcription	Psoas Muscle	Psoas
28	chr8:6567400-6590800	Weak transcription	Pancreas	Pancrea
29	chr8:6567400-6592600	Weak transcription	Aorta	Aorta
30	chr8:6567600-6569000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr8:6567600-6569000	Weak transcription	Fetal Thymus	thymus
32	chr8:6567600-6572800	Weak transcription	Stomach Mucosa	stomach
33	chr8:6567600-6575600	Weak transcription	Fetal Stomach	stomach
34	chr8:6567600-6575600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr8:6567600-6577400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr8:6567600-6585400	Weak transcription	Fetal Intestine Small	intestine
37	chr8:6567600-6586400	Weak transcription	Osteobl	bone
38	chr8:6567600-6589400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr8:6567800-6568400	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr8:6567800-6568400	Enhancers	HSMMtube	muscle
41	chr8:6567800-6568800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr8:6567800-6570400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr8:6567800-6571200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr8:6567800-6575800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr8:6567800-6575800	Weak transcription	Fetal Intestine Large	intestine
46	chr8:6567800-6585400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr8:6567800-6585400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr8:6567800-6589200	Weak transcription	Brain Substantia Nigra	brain
49	chr8:6567800-6590000	Weak transcription	NHLF	lung
50	chr8:6568000-6568400	Flanking Active TSS	Fetal Brain Female	brain

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