Variant report

Variant	rs4957436
Chromosome Location	chr5:41924310-41924311
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:41923310-41926130	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:41917385-41928379	K562	blood:	n/a	n/a
3	POLR2A	chr5:41923981-41926698	GM12891	blood:	n/a	n/a
4	POLR2A	chr5:41923687-41924677	MCF10A-Er-Src	breast:	n/a	n/a
5	CTCF	chr5:41924244-41925979	SK-N-SH	brain:	n/a	chr5:41925328-41925341 chr5:41925326-41925344

No.	Distal block	Cell Line	Cell type
1	chr5:41866693..41874585-chr5:41920680..41930326,14	K562	blood:
2	chr5:41924225..41926765-chr5:41937223..41939726,2	MCF-7	breast:
3	chr5:41864208..41872390-chr5:41920936..41926995,11	K562	blood:
4	chr5:41924171..41926713-chr5:43064683..43066902,2	K562	blood:

Variant related genes	Relation type
FBXO4	TF binding region
ENSG00000083720	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000151876	Chromatin interaction
ENSG00000248668	Chromatin interaction

Extended variants
information (count: 183 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:178)

rs_ID	r²[population]
rs10035434	1.00[EUR][1000 genomes]
rs10040757	1.00[EUR][1000 genomes]
rs10043326	1.00[EUR][1000 genomes]
rs10043371	1.00[EUR][1000 genomes]
rs10045473	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10051322	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10052226	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10053522	1.00[EUR][1000 genomes]
rs10054130	1.00[EUR][1000 genomes]
rs10057546	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10057587	1.00[EUR][1000 genomes]
rs10057645	1.00[EUR][1000 genomes]
rs10059424	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10060170	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062703	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064298	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064380	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10065016	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10065335	1.00[EUR][1000 genomes]
rs10069638	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1006996	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10070201	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10075064	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10075429	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10076689	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10077481	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078011	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10079651	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1027348	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10472357	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10472359	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10473252	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10473255	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10941557	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1118104	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11738956	0.95[EUR][1000 genomes]
rs11739257	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11740524	0.93[ASN][1000 genomes]
rs11741731	1.00[CEU][hapmap]
rs11744279	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11744516	0.81[ASN][1000 genomes]
rs11744623	0.93[ASN][1000 genomes]
rs11745373	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11745460	1.00[EUR][1000 genomes]
rs11745530	1.00[EUR][1000 genomes]
rs11746530	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11747648	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11747921	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11748575	1.00[CEU][hapmap]
rs11748578	1.00[CEU][hapmap]
rs11748933	1.00[EUR][1000 genomes]
rs1175227	1.00[ASN][1000 genomes]
rs13353950	1.00[CEU][hapmap]
rs13355194	1.00[EUR][1000 genomes]
rs13357951	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13357980	1.00[CEU][hapmap]
rs13358459	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13360001	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13436920	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap]
rs1355089	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1508816	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1533014	0.93[ASN][1000 genomes]
rs1567323	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16871972	0.93[ASN][1000 genomes]
rs16872052	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17339188	1.00[EUR][1000 genomes]
rs17739462	0.93[ASN][1000 genomes]
rs17847285	0.93[ASN][1000 genomes]
rs1876654	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2113053	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231910	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231917	1.00[ASN][1000 genomes]
rs2329815	0.93[ASN][1000 genomes]
rs277406	1.00[ASN][1000 genomes]
rs277407	1.00[ASN][1000 genomes]
rs277414	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs277416	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28647448	1.00[EUR][1000 genomes]
rs316746	0.87[EUR][1000 genomes]
rs34339137	0.93[ASN][1000 genomes]
rs34493032	1.00[EUR][1000 genomes]
rs34663371	0.93[ASN][1000 genomes]
rs35077044	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs35154057	0.93[ASN][1000 genomes]
rs35252930	0.81[ASN][1000 genomes]
rs35613904	0.93[ASN][1000 genomes]
rs35890705	1.00[EUR][1000 genomes]
rs3863160	0.82[AMR][1000 genomes]
rs4050986	0.93[ASN][1000 genomes]
rs4289604	1.00[ASN][1000 genomes]
rs4324728	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4957171	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957173	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957174	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957175	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957176	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957177	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957178	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957180	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957182	0.92[AMR][1000 genomes]
rs4957422	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957423	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957424	0.93[ASN][1000 genomes]
rs4957428	0.93[ASN][1000 genomes]
rs4957429	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957430	0.93[ASN][1000 genomes]
rs4957431	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957432	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957433	1.00[ASN][1000 genomes]
rs4957434	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4957435	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957437	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957438	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957439	1.00[ASN][1000 genomes]
rs57944767	0.90[EUR][1000 genomes]
rs582920	0.92[EUR][1000 genomes]
rs583090	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs584067	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs590851	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs591384	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs602274	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs607620	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61058110	0.95[EUR][1000 genomes]
rs621944	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs626907	1.00[JPT][hapmap]
rs627476	0.87[EUR][1000 genomes]
rs641270	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6451582	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs654400	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs66820325	0.93[ASN][1000 genomes]
rs67114999	0.93[ASN][1000 genomes]
rs67152480	0.95[EUR][1000 genomes]
rs676067	1.00[ASN][1000 genomes]
rs678061	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6881873	0.93[ASN][1000 genomes]
rs6889217	1.00[JPT][hapmap]
rs72746926	0.95[EUR][1000 genomes]
rs72746928	0.95[EUR][1000 genomes]
rs72746930	0.95[EUR][1000 genomes]
rs72746932	0.95[EUR][1000 genomes]
rs72746933	0.93[EUR][1000 genomes]
rs72746952	0.95[EUR][1000 genomes]
rs72746962	0.90[EUR][1000 genomes]
rs72746966	0.95[EUR][1000 genomes]
rs72746968	0.95[EUR][1000 genomes]
rs72746975	0.95[EUR][1000 genomes]
rs72746983	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72746985	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72746995	1.00[EUR][1000 genomes]
rs72746996	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72746997	0.95[EUR][1000 genomes]
rs72746999	1.00[EUR][1000 genomes]
rs72747000	1.00[EUR][1000 genomes]
rs72747001	1.00[EUR][1000 genomes]
rs72747002	1.00[EUR][1000 genomes]
rs72748607	1.00[EUR][1000 genomes]
rs72748608	1.00[EUR][1000 genomes]
rs72748609	1.00[EUR][1000 genomes]
rs72748611	1.00[EUR][1000 genomes]
rs72748613	1.00[EUR][1000 genomes]
rs72748614	1.00[EUR][1000 genomes]
rs72748616	1.00[EUR][1000 genomes]
rs72748619	1.00[EUR][1000 genomes]
rs72748620	1.00[EUR][1000 genomes]
rs72748623	0.83[EUR][1000 genomes]
rs7341062	1.00[EUR][1000 genomes]
rs7712106	1.00[EUR][1000 genomes]
rs7712911	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7723992	1.00[EUR][1000 genomes]
rs7728482	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7729014	0.93[ASN][1000 genomes]
rs7733096	0.93[ASN][1000 genomes]
rs9292825	0.86[ASN][1000 genomes]
rs9292826	0.95[EUR][1000 genomes]
rs9292828	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs9292832	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9885033	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9885117	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762518	chr5:41780210-41935113	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	108 gene(s)	inside rSNPs	diseases
2	nsv830272	chr5:41833365-41986167	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
3	nsv830273	chr5:41867296-42066070	Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
4	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
5	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41905000-41924800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:41905200-41925000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:41905600-41924600	Weak transcription	Small Intestine	intestine
4	chr5:41905800-41924400	Weak transcription	Stomach Mucosa	stomach
5	chr5:41905800-41925000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:41905800-41925000	Weak transcription	Gastric	stomach
7	chr5:41906800-41924600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:41909200-41924600	Weak transcription	Fetal Heart	heart
9	chr5:41913200-41925000	Weak transcription	Esophagus	oesophagus
10	chr5:41913400-41925000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:41914800-41924800	Weak transcription	Pancreas	Pancrea
12	chr5:41915200-41925000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:41915800-41924600	Weak transcription	Brain Angular Gyrus	brain
14	chr5:41916000-41924800	Weak transcription	Right Ventricle	heart
15	chr5:41916000-41925000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:41917400-41924800	Weak transcription	Colonic Mucosa	Colon
17	chr5:41918600-41924800	Weak transcription	Fetal Brain Male	brain
18	chr5:41919000-41924400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr5:41919000-41924400	Weak transcription	NHDF-Ad	bronchial
20	chr5:41919000-41924600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:41919000-41924600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:41919000-41924600	Weak transcription	Fetal Intestine Small	intestine
23	chr5:41919000-41924800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr5:41919400-41924400	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:41919600-41924600	Weak transcription	Fetal Stomach	stomach
26	chr5:41919800-41924800	Weak transcription	Aorta	Aorta
27	chr5:41920000-41924600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr5:41920000-41924800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr5:41920000-41924800	Weak transcription	NHLF	lung
30	chr5:41920200-41924600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr5:41920200-41924600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr5:41920200-41924800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr5:41920200-41924800	Weak transcription	Lung	lung
34	chr5:41920400-41924400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr5:41920400-41924600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr5:41920400-41924600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr5:41920400-41924800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr5:41920400-41924800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:41920400-41925400	Weak transcription	Spleen	Spleen
40	chr5:41920600-41924400	Weak transcription	Fetal Muscle Leg	muscle
41	chr5:41920600-41924600	Weak transcription	HSMM	muscle
42	chr5:41920600-41924800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr5:41920800-41924400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr5:41920800-41924600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:41920800-41924600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr5:41920800-41924600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr5:41920800-41924800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:41920800-41924800	Weak transcription	Fetal Kidney	kidney
49	chr5:41920800-41924800	Weak transcription	Placenta	Placenta
50	chr5:41920800-41924800	Weak transcription	Psoas Muscle	Psoas

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