Variant report

Variant	rs10421589
Chromosome Location	chr19:52737267-52737268
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	chr19:52737180-52737378	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52732749..52736646-chr19:52736909..52741775,7	K562	blood:
2	chr19:52725400..52727782-chr19:52737067..52738597,2	K562	blood:

Variant related genes	Relation type
ENSG00000268015	TF binding region
ENSG00000268015	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10402209	0.87[ASN][1000 genomes]
rs10402638	0.87[ASN][1000 genomes]
rs10403202	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10403283	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10403311	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10403464	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10403806	0.87[ASN][1000 genomes]
rs10404437	0.87[ASN][1000 genomes]
rs10407063	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10407502	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10408119	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10411211	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10412110	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10412196	0.83[ASN][1000 genomes]
rs10413012	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10413435	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10414083	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10414197	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10414423	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10414536	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10414852	0.87[ASN][1000 genomes]
rs10416785	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10417033	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10417253	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10418666	0.95[ASN][1000 genomes]
rs10420207	0.98[ASN][1000 genomes]
rs10420560	0.87[ASN][1000 genomes]
rs10421440	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10422483	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10422838	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10423125	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10425135	0.87[ASN][1000 genomes]
rs10426002	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10426786	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16983598	0.87[ASN][1000 genomes]
rs16983601	0.87[ASN][1000 genomes]
rs16983603	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16983610	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17835942	0.91[EUR][1000 genomes]
rs2115074	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28444225	0.86[ASN][1000 genomes]
rs28563055	0.86[ASN][1000 genomes]
rs55751302	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55871532	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57102373	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60063830	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6509628	0.87[ASN][1000 genomes]
rs7249460	0.89[ASN][1000 genomes]
rs7255058	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7255677	0.85[ASN][1000 genomes]
rs7255737	0.87[ASN][1000 genomes]
rs7256125	0.86[ASN][1000 genomes]
rs7256216	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7256300	0.86[ASN][1000 genomes]
rs7256312	0.86[ASN][1000 genomes]
rs7256719	0.86[ASN][1000 genomes]
rs7259175	0.83[ASN][1000 genomes]
rs73935052	0.87[ASN][1000 genomes]
rs73935053	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8100048	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8100600	0.91[EUR][1000 genomes]
rs8101990	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8105432	0.87[ASN][1000 genomes]
rs8106271	0.91[EUR][1000 genomes]
rs8106544	0.93[ASN][1000 genomes]
rs8108636	0.87[ASN][1000 genomes]
rs8109512	0.87[ASN][1000 genomes]
rs8110857	0.87[ASN][1000 genomes]
rs8110881	0.87[ASN][1000 genomes]
rs874421	0.91[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	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv962989	chr19:52732337-52742183	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52727600-52737800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr19:52730200-52737800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr19:52730800-52741000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:52731600-52738000	Weak transcription	Fetal Brain Male	brain
5	chr19:52731600-52741000	Weak transcription	Colon Smooth Muscle	Colon
6	chr19:52732000-52740600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr19:52732000-52740800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:52732200-52741000	Weak transcription	Dnd41	blood
9	chr19:52732200-52741200	Weak transcription	Fetal Lung	lung
10	chr19:52732400-52737800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:52732400-52737800	Weak transcription	HepG2	liver
12	chr19:52732400-52740200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:52732400-52740600	Weak transcription	Brain Angular Gyrus	brain
14	chr19:52732400-52741000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr19:52732400-52741200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr19:52733000-52737400	Weak transcription	Colonic Mucosa	Colon
17	chr19:52733200-52742800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:52733200-52759600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:52733400-52741200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr19:52734200-52741000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:52734400-52751600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr19:52734600-52740800	Weak transcription	Fetal Stomach	stomach
23	chr19:52734600-52743800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr19:52735000-52740400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:52735200-52738800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:52735200-52740600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr19:52735200-52741200	Weak transcription	Fetal Muscle Leg	muscle

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