Variant report

Variant	rs3825627
Chromosome Location	chr14:45572528-45572529
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:45552219..45555964-chr14:45571597..45574194,3	MCF-7	breast:
2	chr14:45571772..45573660-chr14:45574172..45575823,2	MCF-7	breast:
3	chr14:45572072..45577375-chr14:45579640..45584975,5	MCF-7	breast:
4	chr14:45551561..45554829-chr14:45572115..45575358,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239043	Chromatin interaction
ENSG00000185246	Chromatin interaction
ENSG00000249163	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10130368	0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs10130377	0.84[JPT][hapmap];0.89[EUR][1000 genomes]
rs10131066	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10131615	0.89[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes]
rs10132389	0.86[AMR][1000 genomes]
rs10132547	0.89[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes]
rs10132949	0.89[JPT][hapmap];1.00[MEX][hapmap]
rs10134071	0.89[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10134598	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10135085	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10135890	0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs10136008	0.80[EUR][1000 genomes]
rs10138272	0.88[JPT][hapmap]
rs10138997	0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs10140049	0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs10140222	0.89[JPT][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes]
rs10140318	0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs10141474	0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs10143806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10145092	0.88[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs10145267	0.89[JPT][hapmap]
rs10146395	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10147499	0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10152101	0.89[JPT][hapmap];1.00[MEX][hapmap]
rs1053667	0.89[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs11157423	0.89[JPT][hapmap]
rs11157424	0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs11844832	0.89[JPT][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs11845088	0.89[JPT][hapmap]
rs11845904	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs11845956	0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11846656	0.83[TSI][hapmap]
rs11847336	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11848334	0.82[CEU][hapmap]
rs11848799	0.89[JPT][hapmap];0.83[TSI][hapmap]
rs11849208	0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs11850363	0.89[JPT][hapmap]
rs11851962	0.82[CEU][hapmap]
rs11852210	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs12100842	0.89[CHD][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17115703	0.89[JPT][hapmap]
rs17115718	0.89[JPT][hapmap]
rs17115787	1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17115809	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17115811	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2016738	1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2033385	0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs28370281	0.91[EUR][1000 genomes]
rs28448551	0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28572336	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28594810	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28622413	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28637857	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28681969	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3783700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3783702	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3825625	0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs3825628	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825629	0.89[JPT][hapmap]
rs4141578	0.89[JPT][hapmap]
rs56706956	0.82[EUR][1000 genomes]
rs56836063	0.89[EUR][1000 genomes]
rs57003561	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57602646	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57614513	0.82[EUR][1000 genomes]
rs57694277	0.82[EUR][1000 genomes]
rs58826926	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59353994	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60891427	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61155826	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61707578	0.82[EUR][1000 genomes]
rs6572290	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs7145831	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs7146566	0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7147644	0.89[JPT][hapmap]
rs7158846	0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs72474138	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73334913	0.82[EUR][1000 genomes]
rs73340611	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73340622	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73340626	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73340655	0.91[EUR][1000 genomes]
rs73340659	0.91[EUR][1000 genomes]
rs73348065	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73348069	0.82[EUR][1000 genomes]
rs73348076	0.82[EUR][1000 genomes]
rs73348079	0.82[EUR][1000 genomes]
rs73348088	0.82[EUR][1000 genomes]
rs73348095	0.82[EUR][1000 genomes]
rs73349820	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73349835	0.96[ASN][1000 genomes]
rs73349842	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73349853	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73349857	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73349858	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73349868	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73352233	0.82[EUR][1000 genomes]
rs7493823	0.82[EUR][1000 genomes]
rs8006685	0.89[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes]
rs8009193	0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs8015453	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8017844	0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs8022008	0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs8022499	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8022608	0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9323106	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv1794986	chr14:45368685-45650813	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	esv1800510	chr14:45572528-45650813	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3825627	FANCM	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:45554000-45585400	Weak transcription	Gastric	stomach
2	chr14:45554400-45578800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:45554400-45585400	Weak transcription	Esophagus	oesophagus
4	chr14:45554600-45576600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr14:45554600-45602600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr14:45555000-45577000	Weak transcription	Aorta	Aorta
7	chr14:45555000-45586200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:45555200-45579000	Weak transcription	Stomach Mucosa	stomach
9	chr14:45555400-45574600	Weak transcription	Ovary	ovary
10	chr14:45555800-45573600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr14:45556200-45573800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr14:45556400-45582000	Weak transcription	Fetal Brain Male	brain
13	chr14:45557400-45602200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr14:45559000-45591800	Weak transcription	Small Intestine	intestine
15	chr14:45560200-45582000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr14:45560200-45599800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr14:45562000-45599200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr14:45563400-45579200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr14:45563400-45598600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr14:45563600-45578400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr14:45563600-45579200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr14:45563600-45580400	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr14:45563600-45599600	Strong transcription	Dnd41	blood
24	chr14:45563800-45601600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr14:45564000-45574000	Strong transcription	Primary B cells from cord blood	blood
26	chr14:45564000-45592800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr14:45564000-45595000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr14:45564000-45596200	Strong transcription	Placenta	Placenta
29	chr14:45564000-45599200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr14:45564000-45599800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr14:45564000-45600200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr14:45564200-45581200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr14:45564200-45582200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr14:45564200-45589200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr14:45564200-45593400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr14:45564200-45599200	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr14:45564200-45599200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr14:45564200-45599200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr14:45564200-45601600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr14:45564400-45572800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr14:45564400-45573600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr14:45564400-45574400	Strong transcription	HepG2	liver
43	chr14:45564400-45579200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr14:45564400-45581000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr14:45564400-45582000	Strong transcription	Osteobl	bone
46	chr14:45564400-45582400	Strong transcription	Liver	Liver
47	chr14:45564400-45593400	Strong transcription	Adipose Nuclei	Adipose
48	chr14:45564400-45598400	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr14:45564400-45599000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr14:45564400-45599200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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