Variant report

Variant	rs1252960
Chromosome Location	chr14:45719423-45719424
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
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];0.93[YRI][hapmap];0.83[EUR][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];0.97[YRI][hapmap];0.81[EUR][1000 genomes]
rs10138997	0.86[CHB][hapmap]
rs10141474	0.85[CHB][hapmap]
rs10142759	0.83[EUR][1000 genomes]
rs10143508	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs10143794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10149578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10151937	0.84[EUR][1000 genomes]
rs10220594	0.83[EUR][1000 genomes]
rs11157433	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11845507	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs12433547	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12433565	1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1252957	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252963	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1266209	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1268576	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]
rs1367580	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs1431050	0.86[CHB][hapmap]
rs17115860	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs17115912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17636302	1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.87[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[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28531936	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34101857	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3736772	0.89[CHB][hapmap]
rs3825624	1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3825625	0.86[CHB][hapmap]
rs3916169	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4900665	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4900666	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4900667	1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4906564	0.89[CHB][hapmap]
rs4906566	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4906568	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]
rs57607457	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58790242	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6572296	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]
rs7141145	0.80[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs7147246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7148613	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7160373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73350248	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73350255	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8009193	0.86[CHB][hapmap]
rs8010456	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8017844	0.86[CHB][hapmap]
rs8020533	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs911040	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs911041	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1252960	FANCM	cis	multi-tissue	Pritchard

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:45633800-45721200	Weak transcription	Aorta	Aorta
2	chr14:45682000-45721200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:45682400-45720400	Weak transcription	Brain Germinal Matrix	brain
4	chr14:45692200-45719800	Weak transcription	Esophagus	oesophagus
5	chr14:45695000-45721600	Weak transcription	Pancreas	Pancrea
6	chr14:45700200-45719800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr14:45700200-45720800	Weak transcription	Fetal Kidney	kidney
8	chr14:45702400-45721200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr14:45702600-45720400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr14:45704600-45721200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr14:45704800-45721600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr14:45705400-45721200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr14:45707400-45720600	Weak transcription	HSMM	muscle
14	chr14:45708800-45721000	Weak transcription	Fetal Muscle Leg	muscle
15	chr14:45709000-45720600	Weak transcription	Fetal Intestine Large	intestine
16	chr14:45709200-45720400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr14:45709200-45720400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr14:45709200-45721600	Weak transcription	Left Ventricle	heart
19	chr14:45709800-45720600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr14:45710800-45720600	Weak transcription	Fetal Intestine Small	intestine
21	chr14:45715600-45719600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr14:45716600-45720600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr14:45716600-45722000	Weak transcription	Stomach Mucosa	stomach
24	chr14:45717600-45721200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr14:45718000-45720400	Enhancers	Primary T cells fromperipheralblood	blood
26	chr14:45718000-45720600	Enhancers	Primary B cells from peripheral blood	blood
27	chr14:45718000-45721000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr14:45718000-45721400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr14:45718400-45719600	Active TSS	Duodenum Mucosa	Duodenum
30	chr14:45718400-45721000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr14:45718400-45721200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr14:45718600-45719800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr14:45718600-45719800	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr14:45718600-45721200	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr14:45718800-45719800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr14:45718800-45719800	Enhancers	HepG2	liver
37	chr14:45718800-45720000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr14:45718800-45720400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr14:45718800-45720400	Enhancers	Fetal Thymus	thymus
40	chr14:45718800-45720600	Enhancers	Primary T cells from cord blood	blood
41	chr14:45718800-45720600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr14:45718800-45722800	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr14:45718800-45723400	Active TSS	Rectal Smooth Muscle	rectum
44	chr14:45718800-45723800	Active TSS	GM12878-XiMat	blood
45	chr14:45719000-45719800	Active TSS	Ovary	ovary
46	chr14:45719000-45720000	Enhancers	Small Intestine	intestine
47	chr14:45719000-45720800	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr14:45719000-45721000	Weak transcription	Placenta	Placenta
49	chr14:45719000-45721200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr14:45719000-45721600	Weak transcription	Lung	lung

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