Variant report

Variant	rs10423161
Chromosome Location	chr19:39967989-39967990
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	chr19:39967241-39968195	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:39947157-39987373	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:39967847-39969484	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:39967816-39968082	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39897483..39899188-chr19:39966123..39968419,2	MCF-7	breast:
2	chr19:39935972..39937694-chr19:39965602..39968199,3	K562	blood:
3	chr19:39965047..39968880-chr19:39971509..39974367,5	MCF-7	breast:
4	chr19:39967682..39970182-chr19:39997915..39999826,2	K562	blood:

Variant related genes	Relation type
TIMM50	TF binding region
ENSG00000105197	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000196235	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10420073	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10423921	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10426543	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11882744	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1529733	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs45568533	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802030	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803244	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59269050	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61480418	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62120691	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7245986	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7246329	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73035459	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73035461	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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	chr19:39940000-39968000	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr19:39940200-39968600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:39940200-39968600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:39940200-39968800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr19:39940200-39970600	Weak transcription	Fetal Heart	heart
9	chr19:39947200-39968800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr19:39947400-39968000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:39947400-39968000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:39947400-39968000	Strong transcription	Fetal Muscle Trunk	muscle
13	chr19:39947800-39968000	Strong transcription	NHEK	skin
14	chr19:39954200-39968800	Strong transcription	Fetal Muscle Leg	muscle
15	chr19:39954800-39968600	Strong transcription	Fetal Intestine Small	intestine
16	chr19:39955800-39968400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:39962200-39970800	Weak transcription	Psoas Muscle	Psoas
18	chr19:39962800-39970800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:39963000-39970800	Weak transcription	Hela-S3	cervix
20	chr19:39965400-39968800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:39965400-39968800	Strong transcription	Lung	lung
22	chr19:39965600-39970600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr19:39965600-39970600	Weak transcription	Colon Smooth Muscle	Colon
24	chr19:39965600-39970600	Weak transcription	Stomach Mucosa	stomach
25	chr19:39965600-39970800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr19:39965600-39970800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr19:39965600-39970800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr19:39965800-39970800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr19:39965800-39970800	Weak transcription	Fetal Brain Male	brain
30	chr19:39966000-39970600	Weak transcription	Fetal Kidney	kidney
31	chr19:39966000-39970800	Weak transcription	HMEC	breast
32	chr19:39966800-39968200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr19:39967000-39968200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:39967000-39969000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:39967000-39970600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr19:39967200-39970200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr19:39967200-39970400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr19:39967200-39970400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr19:39967200-39970600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:39967200-39970600	Weak transcription	Pancreas	Pancrea
41	chr19:39967200-39970600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr19:39967200-39970800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr19:39967200-39970800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:39967200-39970800	Weak transcription	HSMMtube	muscle
45	chr19:39967200-39971000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:39967200-39971000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:39967200-39971000	Weak transcription	Ovary	ovary
48	chr19:39967200-39971000	Weak transcription	NHLF	lung
49	chr19:39967400-39970000	Weak transcription	Fetal Intestine Large	intestine
50	chr19:39967400-39970600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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