Variant report

Variant	rs59728172
Chromosome Location	chr1:226049074-226049075
allele	G/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	chr1:226048315-226050473	K562	blood:	n/a	n/a
2	POLR2A	chr1:226048403-226049519	K562	blood:	n/a	n/a
3	POLR2A	chr1:226048877-226049506	K562	blood:	n/a	n/a
4	POLR2A	chr1:226048828-226049316	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:226047696..226051078-chr1:226051903..226054074,3	MCF-7	breast:
2	chr1:225969775..225971862-chr1:226048864..226050541,2	K562	blood:
3	chr1:226043689..226047390-chr1:226048474..226050734,4	K562	blood:

Variant related genes	Relation type
TMEM63A	TF binding region
ENSG00000196187	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10047091	0.90[EUR][1000 genomes]
rs10915883	0.89[AFR][1000 genomes]
rs10915886	0.90[AFR][1000 genomes]
rs10915887	0.97[AFR][1000 genomes]
rs10915888	0.97[AFR][1000 genomes]
rs10915889	0.87[AFR][1000 genomes]
rs10915890	0.83[AFR][1000 genomes]
rs12061043	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12070110	0.90[AFR][1000 genomes]
rs12070816	0.90[AFR][1000 genomes]
rs12071072	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12071104	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12071413	0.90[AFR][1000 genomes]
rs12074209	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12074247	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12075664	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077174	0.89[AFR][1000 genomes]
rs12077562	0.90[AFR][1000 genomes]
rs12077565	0.90[AFR][1000 genomes]
rs12079891	0.97[AFR][1000 genomes]
rs12081742	0.94[AFR][1000 genomes]
rs12082207	0.94[AFR][1000 genomes]
rs12083928	0.90[AFR][1000 genomes]
rs12084714	0.90[AFR][1000 genomes]
rs12088057	0.86[AFR][1000 genomes]
rs12091106	0.90[AFR][1000 genomes]
rs12097377	0.94[AFR][1000 genomes]
rs2236143	0.87[EUR][1000 genomes]
rs2271544	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292556	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292559	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292560	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292561	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292568	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28384446	0.92[EUR][1000 genomes]
rs28384447	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28384448	0.95[EUR][1000 genomes]
rs28384449	0.95[EUR][1000 genomes]
rs360084	1.00[ASN][1000 genomes]
rs360087	1.00[ASN][1000 genomes]
rs360089	1.00[ASN][1000 genomes]
rs3738050	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738051	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753663	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753666	0.92[EUR][1000 genomes]
rs3753668	0.90[EUR][1000 genomes]
rs3753670	0.90[EUR][1000 genomes]
rs3766935	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766936	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766937	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766940	0.95[EUR][1000 genomes]
rs3766941	0.90[EUR][1000 genomes]
rs3806257	0.90[EUR][1000 genomes]
rs3806258	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41310561	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4149227	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4149228	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4149230	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs45467394	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55706532	0.87[AFR][1000 genomes]
rs56112955	0.94[AFR][1000 genomes]
rs56231004	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56301120	0.99[ASN][1000 genomes]
rs56325807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57095220	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57932384	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58852301	0.90[AFR][1000 genomes]
rs60739570	0.94[AFR][1000 genomes]
rs60847271	0.95[EUR][1000 genomes]
rs60943392	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61033712	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61227102	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61295362	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61304305	0.90[AFR][1000 genomes]
rs6664740	0.90[EUR][1000 genomes]
rs74150536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74150537	0.95[AFR][1000 genomes]
rs74150538	0.97[AFR][1000 genomes]
rs74150539	0.94[AFR][1000 genomes]
rs7514448	0.90[EUR][1000 genomes]
rs7516538	0.90[EUR][1000 genomes]
rs805179	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv520628	chr1:226026406-226093362	Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226013600-226052600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:226016000-226051000	Weak transcription	NH-A	brain
3	chr1:226017400-226049800	Weak transcription	HUVEC	blood vessel
4	chr1:226026800-226061600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:226029800-226050600	Strong transcription	Right Ventricle	heart
6	chr1:226030400-226052600	Weak transcription	HSMMtube	muscle
7	chr1:226033600-226053000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:226033800-226067400	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr1:226034000-226056800	Strong transcription	Adipose Nuclei	Adipose
10	chr1:226034000-226063000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:226034200-226062800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:226036600-226064600	Weak transcription	Fetal Heart	heart
13	chr1:226036800-226058600	Weak transcription	Brain Germinal Matrix	brain
14	chr1:226036800-226066600	Weak transcription	Fetal Brain Male	brain
15	chr1:226037000-226054200	Weak transcription	Small Intestine	intestine
16	chr1:226037400-226051800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:226037600-226051800	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr1:226037600-226060600	Strong transcription	Placenta	Placenta
19	chr1:226037800-226065200	Weak transcription	Right Atrium	heart
20	chr1:226038000-226052400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:226038400-226059600	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:226038600-226054800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:226038800-226065800	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:226039000-226063200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:226039200-226064600	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:226039400-226053000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:226039400-226053200	Strong transcription	Thymus	Thymus
28	chr1:226039600-226050800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:226039600-226051200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:226039600-226053800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:226039600-226059800	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:226039600-226062200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:226039600-226063000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:226039800-226050400	Strong transcription	Colon Smooth Muscle	Colon
35	chr1:226039800-226052000	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:226039800-226053800	Strong transcription	Fetal Stomach	stomach
37	chr1:226040000-226049800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr1:226040000-226051000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:226040200-226051000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:226040200-226051400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:226040400-226052000	Strong transcription	Ovary	ovary
42	chr1:226040400-226053400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:226040600-226053000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:226040600-226053400	Strong transcription	Primary T cells from cord blood	blood
45	chr1:226040800-226052200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
46	chr1:226040800-226053400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:226040800-226053400	Weak transcription	HMEC	breast
48	chr1:226041000-226053000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:226041000-226053000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr1:226041200-226053800	Strong transcription	Fetal Muscle Trunk	muscle

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