Variant report

Variant	rs73035461
Chromosome Location	chr19:39968513-39968514
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	chr19:39947157-39987373	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:39968164-39969465	GM12891	blood:	n/a	n/a
3	POLR2A	chr19:39968195-39968830	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:39967847-39969484	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:39968259-39968767	GM12891	blood:	n/a	n/a
6	POLR2A	chr19:39968496-39968738	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:39968137-39968882	GM12892	blood:	n/a	n/a
8	POLR2A	chr19:39968466-39968744	GM12891	blood:	n/a	n/a
9	POLR2A	chr19:39968371-39968898	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:39968386-39968850	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr19:39968262-39969213	GM12892	blood:	n/a	n/a
12	POLR2A	chr19:39968267-39968862	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39965047..39968880-chr19:39971509..39974367,5	MCF-7	breast:
2	chr19:39967682..39970182-chr19:39997915..39999826,2	K562	blood:
3	chr19:39956900..39963294-chr19:39968062..39973681,7	MCF-7	breast:

Variant related genes	Relation type
TIMM50	TF binding region
ENSG00000196235	Chromatin interaction
ENSG00000105197	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10420073	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10423161	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10423921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10426543	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11882744	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1529733	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs45568533	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802030	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802033	0.80[ASN][1000 genomes]
rs4803238	0.84[EUR][1000 genomes]
rs4803244	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59269050	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61480418	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62120691	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7245986	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7246329	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73035459	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106642	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv544003	chr19:39937078-39974282	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39937000-39971000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39937400-39971000	Weak transcription	Right Atrium	heart
3	chr19:39939400-39968800	Strong transcription	Fetal Stomach	stomach
4	chr19:39940200-39968600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:39940200-39968600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr19:39940200-39968800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr19:39940200-39970600	Weak transcription	Fetal Heart	heart
8	chr19:39947200-39968800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr19:39954200-39968800	Strong transcription	Fetal Muscle Leg	muscle
10	chr19:39954800-39968600	Strong transcription	Fetal Intestine Small	intestine
11	chr19:39962200-39970800	Weak transcription	Psoas Muscle	Psoas
12	chr19:39962800-39970800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:39963000-39970800	Weak transcription	Hela-S3	cervix
14	chr19:39965400-39968800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr19:39965400-39968800	Strong transcription	Lung	lung
16	chr19:39965600-39970600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr19:39965600-39970600	Weak transcription	Colon Smooth Muscle	Colon
18	chr19:39965600-39970600	Weak transcription	Stomach Mucosa	stomach
19	chr19:39965600-39970800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:39965600-39970800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr19:39965600-39970800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr19:39965800-39970800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr19:39965800-39970800	Weak transcription	Fetal Brain Male	brain
24	chr19:39966000-39970600	Weak transcription	Fetal Kidney	kidney
25	chr19:39966000-39970800	Weak transcription	HMEC	breast
26	chr19:39967000-39969000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr19:39967000-39970600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr19:39967200-39970200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr19:39967200-39970400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr19:39967200-39970400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr19:39967200-39970600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr19:39967200-39970600	Weak transcription	Pancreas	Pancrea
33	chr19:39967200-39970600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr19:39967200-39970800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr19:39967200-39970800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:39967200-39970800	Weak transcription	HSMMtube	muscle
37	chr19:39967200-39971000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:39967200-39971000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr19:39967200-39971000	Weak transcription	Ovary	ovary
40	chr19:39967200-39971000	Weak transcription	NHLF	lung
41	chr19:39967400-39970000	Weak transcription	Fetal Intestine Large	intestine
42	chr19:39967400-39970600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr19:39967400-39970600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr19:39967400-39970600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:39967400-39970600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr19:39967400-39970600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr19:39967400-39970600	Weak transcription	Brain Hippocampus Middle	brain
48	chr19:39967400-39970600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr19:39967400-39970600	Weak transcription	Thymus	Thymus
50	chr19:39967400-39970600	Weak transcription	HepG2	liver

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