Variant report

Variant	rs6572296
Chromosome Location	chr14:45666497-45666498
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10129236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10130368	1.00[CHB][hapmap]
rs10130377	1.00[CHB][hapmap]
rs10134598	0.82[MKK][hapmap]
rs10137415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10138997	1.00[CHB][hapmap]
rs10141474	1.00[CHB][hapmap]
rs10142759	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10143508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10143794	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10149578	1.00[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10151937	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10220594	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11157433	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11845507	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12100842	0.82[MKK][hapmap]
rs12433547	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs12433565	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs1252957	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1252959	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1252960	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1252963	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1252966	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1266209	0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1268576	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs1367580	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1431050	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[EUR][1000 genomes]
rs17115860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17115912	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17636302	0.86[CHB][hapmap]
rs1969713	0.82[EUR][1000 genomes]
rs2033385	1.00[CHB][hapmap];0.86[MKK][hapmap]
rs2145148	0.86[CHB][hapmap]
rs2415883	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2750119	1.00[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28421670	0.94[EUR][1000 genomes]
rs28531936	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28637857	0.80[MKK][hapmap]
rs3736772	1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3825624	0.86[CHB][hapmap]
rs3825625	1.00[CHB][hapmap]
rs3916169	0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs4900664	0.86[CHB][hapmap];0.85[CHD][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4900667	0.86[CHB][hapmap]
rs4906564	1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs4906566	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4906568	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57607457	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58790242	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7141145	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7147246	0.85[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7148613	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7160373	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73350248	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8009193	1.00[CHB][hapmap]
rs8010456	0.82[ASN][1000 genomes]
rs8017844	1.00[CHB][hapmap]
rs8020533	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs911040	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs911041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6572296	FANCM	cis	lymphoblastoid	seeQTL
rs6572296	FANCM	cis	multi-tissue	Pritchard

Chromatin state (count:103 , 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	chr14:45608400-45668400	Weak transcription	NHDF-Ad	bronchial
5	chr14:45610200-45667400	Weak transcription	HMEC	breast
6	chr14:45614400-45675000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr14:45629800-45680800	Weak transcription	HepG2	liver
8	chr14:45630800-45704400	Weak transcription	Fetal Brain Male	brain
9	chr14:45631000-45675000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr14:45631800-45711400	Weak transcription	Brain Hippocampus Middle	brain
11	chr14:45632800-45707000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr14:45633800-45721200	Weak transcription	Aorta	Aorta
13	chr14:45635200-45678400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr14:45635200-45678800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr14:45636000-45669800	Weak transcription	Fetal Stomach	stomach
16	chr14:45636000-45675400	Weak transcription	Fetal Intestine Small	intestine
17	chr14:45636400-45673800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr14:45636400-45675600	Weak transcription	Fetal Muscle Leg	muscle
19	chr14:45636600-45667600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr14:45636600-45669800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr14:45636600-45675600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr14:45636600-45682800	Weak transcription	Fetal Lung	lung
23	chr14:45636800-45670600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr14:45636800-45671400	Weak transcription	Placenta	Placenta
25	chr14:45637000-45669600	Weak transcription	Hela-S3	cervix
26	chr14:45637000-45670600	Weak transcription	A549	lung
27	chr14:45637200-45671000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr14:45637600-45673200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr14:45639400-45667400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr14:45643400-45681000	Weak transcription	Pancreas	Pancrea
31	chr14:45643800-45692800	Weak transcription	Fetal Kidney	kidney
32	chr14:45645600-45671200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr14:45651400-45667600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr14:45651600-45667800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr14:45651800-45667200	Weak transcription	NH-A	brain
36	chr14:45654200-45680400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr14:45654600-45675600	Weak transcription	Thymus	Thymus
38	chr14:45655200-45675600	Weak transcription	Lung	lung
39	chr14:45655600-45667800	Weak transcription	HSMMtube	muscle
40	chr14:45655600-45719200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr14:45655800-45680800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr14:45656200-45679400	Weak transcription	Fetal Brain Female	brain
43	chr14:45656600-45675000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr14:45656600-45691800	Weak transcription	Small Intestine	intestine
45	chr14:45656800-45667800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr14:45657000-45681000	Weak transcription	Brain Angular Gyrus	brain
47	chr14:45657000-45681000	Weak transcription	Esophagus	oesophagus
48	chr14:45657000-45681200	Weak transcription	Brain Germinal Matrix	brain
49	chr14:45657000-45681400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr14:45657200-45683400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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