Variant report

Variant	rs1268576
Chromosome Location	chr14:45713174-45713175
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:45705828..45707853-chr14:45712067..45713833,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10129236	0.88[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs10130368	0.86[CHB][hapmap]
rs10130377	0.82[CHB][hapmap]
rs10137415	0.89[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs10138997	0.86[CHB][hapmap]
rs10141474	0.82[CHB][hapmap]
rs10142759	0.83[EUR][1000 genomes]
rs10143508	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs10143794	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]
rs10149578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10151937	0.84[EUR][1000 genomes]
rs10220594	0.83[EUR][1000 genomes]
rs11157433	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs11845507	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs12433547	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12433565	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1252957	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252966	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[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]
rs1266209	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1367580	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs1431050	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs17115860	0.93[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs17115912	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17636302	1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2033385	0.86[CHB][hapmap]
rs2145148	1.00[CHB][hapmap]
rs2415883	0.82[EUR][1000 genomes]
rs2750119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28531936	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34101857	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3736772	0.86[CHB][hapmap]
rs3825624	1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3825625	0.86[CHB][hapmap]
rs3916169	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4900664	0.85[CHD][hapmap]
rs4900665	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4900666	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4900667	1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4906564	0.86[CHB][hapmap]
rs4906566	0.83[EUR][1000 genomes]
rs4906568	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs57607457	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58790242	0.83[EUR][1000 genomes]
rs6572296	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]
rs7141145	0.80[CEU][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs7147246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7148613	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs7160373	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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]
rs73350248	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73350255	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8009193	0.86[CHB][hapmap]
rs8010456	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8017844	0.86[CHB][hapmap]
rs8020533	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs911040	0.83[EUR][1000 genomes]
rs911041	0.93[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv901846	chr14:45702358-45783546	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv564726	chr14:45702358-45911581	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	esv2758357	chr14:45706082-45982410	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	esv2759987	chr14:45706082-45982410	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1268576	FANCM	cis	lymphoblastoid	seeQTL
rs1268576	FANCM	cis	multi-tissue	Pritchard

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:45633800-45721200	Weak transcription	Aorta	Aorta
2	chr14:45655600-45719200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr14:45674600-45719200	Weak transcription	Colonic Mucosa	Colon
4	chr14:45680400-45714000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr14:45682000-45721200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr14:45682200-45714800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr14:45682200-45719200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr14:45682400-45720400	Weak transcription	Brain Germinal Matrix	brain
9	chr14:45684800-45719400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr14:45686600-45719200	Weak transcription	Fetal Heart	heart
11	chr14:45687200-45719200	Weak transcription	HSMMtube	muscle
12	chr14:45691600-45713800	Strong transcription	Primary B cells from peripheral blood	blood
13	chr14:45692200-45719000	Weak transcription	Small Intestine	intestine
14	chr14:45692200-45719800	Weak transcription	Esophagus	oesophagus
15	chr14:45692800-45718600	Weak transcription	Lung	lung
16	chr14:45693600-45719200	Weak transcription	K562	blood
17	chr14:45693600-45719200	Weak transcription	NHEK	skin
18	chr14:45695000-45721600	Weak transcription	Pancreas	Pancrea
19	chr14:45699600-45715200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr14:45699800-45715200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr14:45700200-45715000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr14:45700200-45719800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr14:45700200-45720800	Weak transcription	Fetal Kidney	kidney
24	chr14:45701000-45716000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr14:45701000-45718600	Weak transcription	Placenta	Placenta
26	chr14:45701000-45719200	Weak transcription	Liver	Liver
27	chr14:45702400-45721200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr14:45702600-45719200	Weak transcription	Fetal Lung	lung
29	chr14:45702600-45720400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr14:45702800-45719200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr14:45702800-45719200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr14:45704000-45715400	Weak transcription	NHDF-Ad	bronchial
33	chr14:45704000-45716000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr14:45704200-45719000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr14:45704600-45715200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr14:45704600-45715200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr14:45704600-45719000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr14:45704600-45721200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr14:45704800-45718800	Weak transcription	Fetal Stomach	stomach
40	chr14:45704800-45721600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr14:45705000-45718600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr14:45705200-45719200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr14:45705400-45721200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr14:45706400-45715200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr14:45707400-45720600	Weak transcription	HSMM	muscle
46	chr14:45708600-45716000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr14:45708800-45721000	Weak transcription	Fetal Muscle Leg	muscle
48	chr14:45709000-45715800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr14:45709000-45719200	Weak transcription	NH-A	brain
50	chr14:45709000-45720600	Weak transcription	Fetal Intestine Large	intestine

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