Variant report

Variant	rs10059424
Chromosome Location	chr5:41906206-41906207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:41867500..41871930-chr5:41901815..41908844,17	K562	blood:
2	chr5:40909913..40911459-chr5:41904598..41906410,2	K562	blood:
3	chr5:41865404..41878163-chr5:41900217..41908471,28	K562	blood:
4	chr5:41905678..41908829-chr5:41924042..41927034,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151876	Chromatin interaction
ENSG00000248668	Chromatin interaction
ENSG00000253098	Chromatin interaction
ENSG00000083720	Chromatin interaction

Extended variants
information (count: 194 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:188)

rs_ID	r²[population]
rs10035434	0.97[EUR][1000 genomes]
rs10040757	0.97[EUR][1000 genomes]
rs10043326	0.97[EUR][1000 genomes]
rs10043371	0.97[EUR][1000 genomes]
rs10045473	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10051322	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10052226	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10053522	0.97[EUR][1000 genomes]
rs10054130	0.97[EUR][1000 genomes]
rs10057546	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10057587	0.97[EUR][1000 genomes]
rs10057645	0.97[EUR][1000 genomes]
rs10060170	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062703	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064298	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064380	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10065016	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10065335	0.97[EUR][1000 genomes]
rs10069638	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1006996	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10070201	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10075064	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10075429	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10076689	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10077481	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078011	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10079651	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1027348	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10472357	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10472359	0.85[EUR][1000 genomes]
rs10473252	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10473255	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10941557	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1118104	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11738956	0.93[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	0.97[EUR][1000 genomes]
rs11745530	0.97[EUR][1000 genomes]
rs11746530	0.97[EUR][1000 genomes]
rs11747648	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11747921	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11748575	1.00[CEU][hapmap]
rs11748578	1.00[CEU][hapmap]
rs11748933	0.97[EUR][1000 genomes]
rs1175227	1.00[ASN][1000 genomes]
rs13353950	1.00[CEU][hapmap]
rs13355194	0.97[EUR][1000 genomes]
rs13357951	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13357980	1.00[CEU][hapmap]
rs13358459	0.97[EUR][1000 genomes]
rs13360001	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13436920	1.00[CEU][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	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16871972	0.93[ASN][1000 genomes]
rs16872052	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs170299	0.85[EUR][1000 genomes]
rs17339188	0.97[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	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231910	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[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[JPT][hapmap];1.00[ASN][1000 genomes]
rs277416	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28647448	0.97[EUR][1000 genomes]
rs316746	0.85[EUR][1000 genomes]
rs316747	0.85[EUR][1000 genomes]
rs316748	0.85[EUR][1000 genomes]
rs316749	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs316750	0.85[EUR][1000 genomes]
rs316752	0.85[EUR][1000 genomes]
rs316754	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs316756	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs316757	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs316758	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34339137	0.93[ASN][1000 genomes]
rs34493032	0.97[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	0.97[EUR][1000 genomes]
rs4050986	0.93[ASN][1000 genomes]
rs4289604	1.00[ASN][1000 genomes]
rs4324728	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	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957180	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957182	0.87[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];0.89[YRI][hapmap]
rs4957435	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957436	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957437	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957438	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957439	1.00[ASN][1000 genomes]
rs57944767	0.88[EUR][1000 genomes]
rs582920	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs583090	0.85[EUR][1000 genomes]
rs584067	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs590851	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs591384	0.83[EUR][1000 genomes]
rs602274	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs607620	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61058110	0.93[EUR][1000 genomes]
rs621944	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs626907	1.00[JPT][hapmap]
rs627476	0.85[EUR][1000 genomes]
rs641270	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6451582	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs654400	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs66820325	0.93[ASN][1000 genomes]
rs67114999	0.93[ASN][1000 genomes]
rs67152480	0.93[EUR][1000 genomes]
rs676067	1.00[ASN][1000 genomes]
rs678061	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6881873	0.93[ASN][1000 genomes]
rs6889217	1.00[JPT][hapmap]
rs72746926	0.93[EUR][1000 genomes]
rs72746928	0.93[EUR][1000 genomes]
rs72746930	0.93[EUR][1000 genomes]
rs72746932	0.93[EUR][1000 genomes]
rs72746933	0.90[EUR][1000 genomes]
rs72746952	0.93[EUR][1000 genomes]
rs72746962	0.88[EUR][1000 genomes]
rs72746966	0.93[EUR][1000 genomes]
rs72746968	0.93[EUR][1000 genomes]
rs72746975	0.93[EUR][1000 genomes]
rs72746983	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72746985	0.97[EUR][1000 genomes]
rs72746995	0.97[EUR][1000 genomes]
rs72746996	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72746997	0.93[EUR][1000 genomes]
rs72746999	0.97[EUR][1000 genomes]
rs72747000	0.97[EUR][1000 genomes]
rs72747001	0.97[EUR][1000 genomes]
rs72747002	0.97[EUR][1000 genomes]
rs72748607	0.97[EUR][1000 genomes]
rs72748608	0.97[EUR][1000 genomes]
rs72748609	0.97[EUR][1000 genomes]
rs72748611	0.97[EUR][1000 genomes]
rs72748613	0.97[EUR][1000 genomes]
rs72748614	0.97[EUR][1000 genomes]
rs72748616	0.97[EUR][1000 genomes]
rs72748619	0.97[EUR][1000 genomes]
rs72748620	0.97[EUR][1000 genomes]
rs72748623	0.81[EUR][1000 genomes]
rs72761834	0.85[EUR][1000 genomes]
rs7341062	0.97[EUR][1000 genomes]
rs7712106	0.97[EUR][1000 genomes]
rs7712911	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7723992	0.97[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	0.93[EUR][1000 genomes]
rs9292828	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9292832	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9885033	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9885117	1.00[CEU][hapmap];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv327668	chr5:41901383-41909830	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41905000-41906800	Transcr. at gene 5' and 3'	K562	blood
2	chr5:41905000-41924800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:41905200-41907000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr5:41905200-41907000	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr5:41905200-41907200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr5:41905200-41908600	Weak transcription	Ovary	ovary
7	chr5:41905200-41912600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:41905200-41912600	Weak transcription	Fetal Stomach	stomach
9	chr5:41905200-41915400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:41905200-41918200	Weak transcription	Aorta	Aorta
11	chr5:41905200-41925000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:41905400-41907000	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr5:41905400-41907200	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr5:41905400-41907200	Enhancers	Brain Substantia Nigra	brain
15	chr5:41905400-41907800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:41905400-41910200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:41905600-41906400	Enhancers	Primary T cells from cord blood	blood
18	chr5:41905600-41906600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:41905600-41907400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
20	chr5:41905600-41907800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr5:41905600-41908000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:41905600-41908200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr5:41905600-41908400	Weak transcription	Colonic Mucosa	Colon
24	chr5:41905600-41908600	Weak transcription	Fetal Brain Female	brain
25	chr5:41905600-41908600	Weak transcription	Fetal Kidney	kidney
26	chr5:41905600-41910000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr5:41905600-41910200	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:41905600-41911200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:41905600-41912600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr5:41905600-41912600	Weak transcription	Lung	lung
31	chr5:41905600-41912600	Weak transcription	Thymus	Thymus
32	chr5:41905600-41912800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr5:41905600-41921000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr5:41905600-41924600	Weak transcription	Small Intestine	intestine
35	chr5:41905800-41906400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:41905800-41906400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr5:41905800-41906400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:41905800-41906400	Enhancers	Liver	Liver
39	chr5:41905800-41906400	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr5:41905800-41906400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr5:41905800-41906400	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr5:41905800-41906400	Active TSS	GM12878-XiMat	blood
43	chr5:41905800-41906400	Weak transcription	Osteobl	bone
44	chr5:41905800-41906600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr5:41905800-41906600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr5:41905800-41906600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr5:41905800-41906600	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr5:41905800-41906600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr5:41905800-41906600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:41905800-41906600	Weak transcription	NHDF-Ad	bronchial

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