Variant report

Variant	rs10143794
Chromosome Location	chr14:45676778-45676779
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	CTCF	chr14:45676762-45676815	MCF-7	breast:	n/a	n/a
2	CTCF	chr14:45676763-45676804	MCF-7	breast:	n/a	n/a
3	POLR2A	chr14:45676753-45677009	MCF-7	breast:	n/a	n/a
4	POLR2A	chr14:45676594-45676897	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
MIS18BP1	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10129236	0.88[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10130368	0.89[CHB][hapmap]
rs10130377	0.84[CHB][hapmap]
rs10137415	0.89[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10138997	0.86[CHB][hapmap]
rs10141474	0.85[CHB][hapmap]
rs10142759	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10143508	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10149578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10151937	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10220594	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11157433	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11845507	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12433547	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs12433565	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs1252957	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1252959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1252960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1252963	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1252966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1266209	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1268576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1367580	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1431050	0.86[CHB][hapmap]
rs17115860	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17115912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17636302	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs2033385	0.86[CHB][hapmap]
rs2145148	1.00[CHB][hapmap]
rs2415883	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2750119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28531936	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34101857	0.87[EUR][1000 genomes]
rs3736772	0.89[CHB][hapmap]
rs3825624	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs3825625	0.86[CHB][hapmap]
rs3916169	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4900665	0.85[EUR][1000 genomes]
rs4900666	0.85[EUR][1000 genomes]
rs4900667	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs4906564	0.89[CHB][hapmap]
rs4906566	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4906568	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57607457	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58790242	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6572296	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7141145	0.80[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7147246	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];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7148613	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7160373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73350248	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73350255	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8009193	0.86[CHB][hapmap]
rs8010456	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8017844	0.86[CHB][hapmap]
rs8020533	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs911040	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs911041	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901841	chr14:45198196-45719643	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv1795667	chr14:45361680-45721052	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1803131	chr14:45441932-45726848	Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv933364	chr14:45467086-45705844	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv901842	chr14:45506857-45713358	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv901843	chr14:45506857-45833490	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv832785	chr14:45520670-45710741	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv530814	chr14:45604432-46198418	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv901844	chr14:45606287-46063731	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv1044445	chr14:45606779-45807171	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv901845	chr14:45619217-45772910	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	nsv1045297	chr14:45631260-45755992	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10143794	FANCM	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:45606000-45679600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr14:45607400-45678400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr14:45608000-45683000	Weak transcription	K562	blood
4	chr14:45629800-45680800	Weak transcription	HepG2	liver
5	chr14:45630800-45704400	Weak transcription	Fetal Brain Male	brain
6	chr14:45631800-45711400	Weak transcription	Brain Hippocampus Middle	brain
7	chr14:45632800-45707000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr14:45633800-45721200	Weak transcription	Aorta	Aorta
9	chr14:45635200-45678400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr14:45635200-45678800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr14:45636600-45682800	Weak transcription	Fetal Lung	lung
12	chr14:45643400-45681000	Weak transcription	Pancreas	Pancrea
13	chr14:45643800-45692800	Weak transcription	Fetal Kidney	kidney
14	chr14:45654200-45680400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr14:45655600-45719200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr14:45655800-45680800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr14:45656200-45679400	Weak transcription	Fetal Brain Female	brain
18	chr14:45656600-45691800	Weak transcription	Small Intestine	intestine
19	chr14:45657000-45681000	Weak transcription	Brain Angular Gyrus	brain
20	chr14:45657000-45681000	Weak transcription	Esophagus	oesophagus
21	chr14:45657000-45681200	Weak transcription	Brain Germinal Matrix	brain
22	chr14:45657000-45681400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:45657200-45683400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr14:45658000-45680800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr14:45658200-45680800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr14:45658600-45678600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr14:45658600-45680800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr14:45658600-45681200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr14:45660600-45679000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr14:45660600-45707000	Weak transcription	Gastric	stomach
31	chr14:45660800-45680800	Weak transcription	Ovary	ovary
32	chr14:45660800-45703400	Weak transcription	Psoas Muscle	Psoas
33	chr14:45661400-45680600	Weak transcription	Spleen	Spleen
34	chr14:45662800-45711400	Weak transcription	Brain Anterior Caudate	brain
35	chr14:45663800-45680600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr14:45664000-45696000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr14:45666600-45680800	Weak transcription	Left Ventricle	heart
38	chr14:45668000-45681000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr14:45668600-45680000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr14:45668600-45681000	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr14:45668600-45683800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr14:45668800-45683400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr14:45669000-45679000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr14:45669000-45679400	Weak transcription	NH-A	brain
45	chr14:45669000-45686800	Weak transcription	HSMMtube	muscle
46	chr14:45669200-45678600	Weak transcription	Osteobl	bone
47	chr14:45669200-45679600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr14:45669200-45680800	Weak transcription	NHEK	skin
49	chr14:45669400-45677600	Strong transcription	Dnd41	blood
50	chr14:45669600-45681400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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