Variant report

Variant	rs1252959
Chromosome Location	chr14:45720603-45720604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:45602054..45606945-chr14:45719959..45724414,9	MCF-7	breast:
2	chr14:45429725..45432587-chr14:45720437..45723992,3	MCF-7	breast:
3	chr14:45603451..45606015-chr14:45719614..45721854,2	K562	blood:

Variant related genes	Relation type
ENSG00000187790	Chromatin interaction
ENSG00000198718	Chromatin interaction
ENSG00000100442	Chromatin interaction
ENSG00000179454	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

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];0.83[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];0.81[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];0.83[EUR][1000 genomes]
rs10143794	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]
rs10149578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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];0.83[EUR][1000 genomes]
rs11845507	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][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	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252960	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	0.98[AFR][1000 genomes];0.98[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];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[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];0.87[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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[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];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs1431050	0.86[CHB][hapmap]
rs17115860	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs17115912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];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];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28531936	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];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	0.83[EUR][1000 genomes]
rs4906568	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs57607457	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58790242	0.83[EUR][1000 genomes]
rs6572296	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];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];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7148613	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs7160373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73350248	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];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];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs911040	0.83[EUR][1000 genomes]
rs911041	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.83[EUR][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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
rs1252959	C14orf106	cis	multi-tissue	Pritchard
rs1252959	FANCM	cis	multi-tissue	Pritchard

Chromatin state (count:113 , 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	chr14:45695000-45721600	Weak transcription	Pancreas	Pancrea
4	chr14:45700200-45720800	Weak transcription	Fetal Kidney	kidney
5	chr14:45702400-45721200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr14:45704600-45721200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr14:45704800-45721600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr14:45705400-45721200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr14:45708800-45721000	Weak transcription	Fetal Muscle Leg	muscle
10	chr14:45709200-45721600	Weak transcription	Left Ventricle	heart
11	chr14:45716600-45722000	Weak transcription	Stomach Mucosa	stomach
12	chr14:45717600-45721200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr14:45718000-45721000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr14:45718000-45721400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr14:45718400-45721000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr14:45718400-45721200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr14:45718600-45721200	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr14:45718800-45722800	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr14:45718800-45723400	Active TSS	Rectal Smooth Muscle	rectum
20	chr14:45718800-45723800	Active TSS	GM12878-XiMat	blood
21	chr14:45719000-45720800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr14:45719000-45721000	Weak transcription	Placenta	Placenta
23	chr14:45719000-45721200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr14:45719000-45721600	Weak transcription	Lung	lung
25	chr14:45719200-45720800	Enhancers	Fetal Heart	heart
26	chr14:45719200-45721000	Flanking Active TSS	Dnd41	blood
27	chr14:45719200-45721600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr14:45719400-45721000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr14:45719600-45721000	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr14:45719600-45721000	Weak transcription	Colonic Mucosa	Colon
31	chr14:45719600-45721000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr14:45719600-45721000	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr14:45719600-45721200	Weak transcription	HSMMtube	muscle
34	chr14:45719600-45721600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr14:45719800-45720800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr14:45719800-45720800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr14:45719800-45721000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr14:45719800-45721000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr14:45719800-45721000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr14:45719800-45721000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr14:45719800-45721000	Weak transcription	Brain Hippocampus Middle	brain
42	chr14:45719800-45721200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr14:45719800-45721200	Weak transcription	Ovary	ovary
44	chr14:45719800-45723200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr14:45720000-45721000	Enhancers	Fetal Lung	lung
46	chr14:45720000-45721200	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr14:45720000-45721800	Weak transcription	Small Intestine	intestine
48	chr14:45720000-45722800	Active TSS	Duodenum Mucosa	Duodenum
49	chr14:45720000-45723000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr14:45720200-45720800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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