Variant report

Variant	rs28637857
Chromosome Location	chr14:45597638-45597639
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:45596796..45599715-chr14:45601507..45604605,3	MCF-7	breast:
2	chr14:45554176..45556075-chr14:45596384..45598770,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100442	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10130368	1.00[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10130377	1.00[CEU][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10131066	0.87[EUR][1000 genomes]
rs10131615	0.88[ASW][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.90[YRI][hapmap]
rs10132389	0.86[YRI][hapmap]
rs10132547	0.88[ASW][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap]
rs10132949	0.88[ASW][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap]
rs10134071	0.88[ASW][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.82[EUR][1000 genomes]
rs10134598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10135085	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10135890	1.00[ASW][hapmap];0.89[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs10136008	0.80[EUR][1000 genomes]
rs10138272	0.88[JPT][hapmap];0.89[YRI][hapmap]
rs10138997	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10140049	0.88[ASW][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.90[YRI][hapmap]
rs10140222	0.88[ASW][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.86[YRI][hapmap];0.82[EUR][1000 genomes]
rs10140318	0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs10141474	1.00[CEU][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10143806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10145092	0.83[ASW][hapmap];0.88[JPT][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs10145267	0.89[JPT][hapmap];0.83[YRI][hapmap]
rs10146395	0.82[EUR][1000 genomes]
rs10147499	0.89[JPT][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs10152101	0.83[ASW][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap]
rs1053667	0.89[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs11157423	0.89[JPT][hapmap];0.80[YRI][hapmap]
rs11157424	0.83[ASW][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap]
rs11157433	0.84[MKK][hapmap]
rs11844832	0.89[JPT][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs11845088	0.89[JPT][hapmap];0.90[YRI][hapmap]
rs11845507	0.84[MKK][hapmap]
rs11845904	0.83[TSI][hapmap]
rs11845956	0.88[ASW][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs11846656	0.83[TSI][hapmap]
rs11847336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11848799	0.89[JPT][hapmap];0.83[TSI][hapmap]
rs11849208	0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs11850363	0.89[JPT][hapmap];0.86[YRI][hapmap]
rs12100842	1.00[ASW][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.99[MKK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17115703	0.89[JPT][hapmap]
rs17115718	0.89[JPT][hapmap];0.83[YRI][hapmap]
rs17115787	0.88[ASW][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.82[EUR][1000 genomes]
rs17115809	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17115811	0.88[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2016738	1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2033385	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28370281	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28448551	0.88[ASW][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs28572336	0.82[EUR][1000 genomes]
rs28594810	0.82[EUR][1000 genomes]
rs28622413	0.82[EUR][1000 genomes]
rs28681969	0.82[EUR][1000 genomes]
rs3783700	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3783702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3825625	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3825627	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]
rs3825628	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3825629	0.89[JPT][hapmap];0.86[YRI][hapmap]
rs4141578	0.89[JPT][hapmap]
rs4906568	0.84[MKK][hapmap]
rs56706956	0.82[EUR][1000 genomes]
rs56836063	0.89[EUR][1000 genomes]
rs57003561	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57602646	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57614513	0.82[EUR][1000 genomes]
rs57694277	0.82[EUR][1000 genomes]
rs58826926	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59353994	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60891427	0.82[EUR][1000 genomes]
rs61155826	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61707578	0.82[EUR][1000 genomes]
rs6572296	0.80[MKK][hapmap]
rs7145831	0.89[JPT][hapmap]
rs7146566	0.89[JPT][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes]
rs7147644	0.89[JPT][hapmap]
rs7148613	0.85[MKK][hapmap]
rs7158846	0.83[ASW][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap]
rs72474138	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73334913	0.82[EUR][1000 genomes]
rs73340611	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73340622	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73340626	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73340655	0.91[EUR][1000 genomes]
rs73340659	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73348065	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	0.89[EUR][1000 genomes]
rs73349835	0.90[ASN][1000 genomes]
rs73349842	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73349853	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73349857	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73349858	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73349868	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73352233	0.82[EUR][1000 genomes]
rs7493823	0.82[EUR][1000 genomes]
rs8006685	0.88[ASW][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.90[YRI][hapmap]
rs8009193	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8015453	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8017844	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8022008	0.88[ASW][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.90[YRI][hapmap]
rs8022499	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8022608	1.00[CEU][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs9323106	0.89[JPT][hapmap];0.90[YRI][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
rs28637857	FANCM	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:45554600-45602600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:45557400-45602200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:45560200-45599800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr14:45562000-45599200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr14:45563400-45598600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr14:45563600-45599600	Strong transcription	Dnd41	blood
7	chr14:45563800-45601600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr14:45564000-45599200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr14:45564000-45599800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr14:45564000-45600200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr14:45564200-45599200	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr14:45564200-45599200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr14:45564200-45599200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr14:45564200-45601600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr14:45564400-45598400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr14:45564400-45599000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr14:45564400-45599200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr14:45564400-45599200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr14:45564400-45599800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr14:45564800-45602200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr14:45573200-45598800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr14:45573800-45602600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr14:45577200-45602800	Weak transcription	Aorta	Aorta
24	chr14:45579800-45599400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr14:45580000-45599200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr14:45581800-45600000	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr14:45582200-45599000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr14:45582800-45598800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr14:45582800-45598800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr14:45583000-45598600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr14:45583000-45599000	Strong transcription	Liver	Liver
32	chr14:45583000-45602800	Weak transcription	Stomach Mucosa	stomach
33	chr14:45583200-45602000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr14:45583800-45602800	Weak transcription	Fetal Brain Male	brain
35	chr14:45584800-45599000	Strong transcription	Fetal Intestine Large	intestine
36	chr14:45585600-45602000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr14:45586400-45602400	Weak transcription	Pancreas	Pancrea
38	chr14:45586600-45602600	Weak transcription	Colonic Mucosa	Colon
39	chr14:45586800-45602800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr14:45589200-45603000	Weak transcription	Gastric	stomach
41	chr14:45589200-45603200	Weak transcription	Spleen	Spleen
42	chr14:45589400-45599800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr14:45589600-45602600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr14:45589800-45600200	Weak transcription	Brain Angular Gyrus	brain
45	chr14:45590200-45598400	Weak transcription	K562	blood
46	chr14:45590200-45599600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr14:45590200-45602000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr14:45590600-45598800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr14:45590600-45601200	Weak transcription	Hela-S3	cervix
50	chr14:45590600-45602600	Weak transcription	Brain Substantia Nigra	brain

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