Variant report

Variant	rs3916169
Chromosome Location	chr14:45717041-45717042
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:45553320..45554876-chr14:45714486..45717051,2	MCF-7	breast:
2	chr14:45710936..45712506-chr14:45717032..45718785,2	K562	blood:

Variant related genes	Relation type
ENSG00000185246	Chromatin interaction
ENSG00000129534	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10129236	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10130368	0.86[CHB][hapmap]
rs10130377	0.82[CHB][hapmap]
rs10137415	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs10138997	0.86[CHB][hapmap]
rs10141474	0.82[CHB][hapmap]
rs10143508	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10143794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10149578	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11157433	0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap]
rs11845507	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap]
rs12433547	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12433565	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1252957	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252963	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252966	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1266209	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1268576	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]
rs1367580	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap]
rs1431050	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs17115860	0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap]
rs17115912	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17636302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2033385	0.86[CHB][hapmap]
rs2145148	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs2750119	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28531936	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34101857	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3736772	0.87[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs3825624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3825625	0.86[CHB][hapmap]
rs4900664	1.00[ASW][hapmap];0.87[CEU][hapmap];0.85[CHD][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs4900665	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4900666	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4900667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4906564	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs4906568	0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap]
rs57607457	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6572296	0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs7141145	1.00[CHD][hapmap];0.81[JPT][hapmap]
rs7147246	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7148613	0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap]
rs7160373	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73350248	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73350255	0.93[ASN][1000 genomes]
rs8009193	0.86[CHB][hapmap]
rs8010456	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8017844	0.86[CHB][hapmap]
rs8020533	0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs911041	0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap]

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
rs3916169	FANCM	cis	lymphoblastoid	seeQTL

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	chr14:45682000-45721200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr14:45682200-45719200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr14:45682400-45720400	Weak transcription	Brain Germinal Matrix	brain
7	chr14:45684800-45719400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:45686600-45719200	Weak transcription	Fetal Heart	heart
9	chr14:45687200-45719200	Weak transcription	HSMMtube	muscle
10	chr14:45692200-45719000	Weak transcription	Small Intestine	intestine
11	chr14:45692200-45719800	Weak transcription	Esophagus	oesophagus
12	chr14:45692800-45718600	Weak transcription	Lung	lung
13	chr14:45693600-45719200	Weak transcription	K562	blood
14	chr14:45693600-45719200	Weak transcription	NHEK	skin
15	chr14:45695000-45721600	Weak transcription	Pancreas	Pancrea
16	chr14:45700200-45719800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr14:45700200-45720800	Weak transcription	Fetal Kidney	kidney
18	chr14:45701000-45718600	Weak transcription	Placenta	Placenta
19	chr14:45701000-45719200	Weak transcription	Liver	Liver
20	chr14:45702400-45721200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr14:45702600-45719200	Weak transcription	Fetal Lung	lung
22	chr14:45702600-45720400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr14:45702800-45719200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr14:45702800-45719200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr14:45704200-45719000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr14:45704600-45719000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr14:45704600-45721200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr14:45704800-45718800	Weak transcription	Fetal Stomach	stomach
29	chr14:45704800-45721600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr14:45705000-45718600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr14:45705200-45719200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr14:45705400-45721200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr14:45707400-45720600	Weak transcription	HSMM	muscle
34	chr14:45708800-45721000	Weak transcription	Fetal Muscle Leg	muscle
35	chr14:45709000-45719200	Weak transcription	NH-A	brain
36	chr14:45709000-45720600	Weak transcription	Fetal Intestine Large	intestine
37	chr14:45709200-45718600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr14:45709200-45719200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr14:45709200-45719200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr14:45709200-45720400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr14:45709200-45720400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr14:45709200-45721600	Weak transcription	Left Ventricle	heart
43	chr14:45709400-45718800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr14:45709600-45718800	Weak transcription	Primary T cells from cord blood	blood
45	chr14:45709800-45720600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr14:45710800-45720600	Weak transcription	Fetal Intestine Small	intestine
47	chr14:45711400-45718400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr14:45711600-45717400	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr14:45711600-45718600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr14:45711600-45719200	Weak transcription	HMEC	breast

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