Variant report

Variant	rs56133747
Chromosome Location	chr1:9665993-9665994
allele	A/G
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	chr1:9665864-9666497	HL-60	blood:	n/a	n/a
2	POLR2A	chr1:9664778-9666137	K562	blood:	n/a	n/a
3	POLR2A	chr1:9665818-9666287	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:9665779-9666021	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:9665600-9666257	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:9665791-9666992	K562	blood:	n/a	n/a
7	POLR2A	chr1:9665584-9666318	Hela-S3	cervix:	n/a	n/a
8	PAX5	chr1:9665899-9666125	GM12878	blood:	n/a	chr1:9665999-9666017
9	POLR2A	chr1:9665388-9666796	K562	blood:	n/a	n/a
10	PAX5	chr1:9665907-9666164	GM12892	blood:	n/a	chr1:9665999-9666017
11	POLR2A	chr1:9665136-9666384	GM12892	blood:	n/a	n/a
12	POLR2A	chr1:9665735-9666164	GM12892	blood:	n/a	n/a
13	POLR2A	chr1:9665838-9666109	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
TMEM201	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10159413	1.00[AMR][1000 genomes]
rs11799995	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11800060	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11804156	0.82[AFR][1000 genomes]
rs11811820	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4073292	1.00[EUR][1000 genomes]
rs4641334	1.00[EUR][1000 genomes]
rs55913306	1.00[AMR][1000 genomes]
rs56674651	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57585081	1.00[AMR][1000 genomes]
rs6701659	1.00[AMR][1000 genomes]
rs74051506	1.00[AMR][1000 genomes]
rs74051508	1.00[AMR][1000 genomes]
rs74051509	1.00[AMR][1000 genomes]
rs74051510	1.00[AMR][1000 genomes]
rs74051513	1.00[AMR][1000 genomes]
rs74051540	1.00[AMR][1000 genomes]
rs74051551	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74051552	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74051558	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74051559	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7518144	0.86[AFR][1000 genomes];1.00[EUR][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	nsv931984	chr1:8879337-9694749	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	570 gene(s)	inside rSNPs	diseases
2	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
3	nsv1013224	chr1:9441040-9699768	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv464283	chr1:9495571-9677853	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv545363	chr1:9495571-9677853	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv871521	chr1:9640291-9666364	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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 target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9650400-9676000	Weak transcription	A549	lung
2	chr1:9651400-9672000	Weak transcription	Hela-S3	cervix
3	chr1:9653800-9675400	Weak transcription	Stomach Mucosa	stomach
4	chr1:9653800-9675800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:9654000-9669800	Weak transcription	NHDF-Ad	bronchial
6	chr1:9654000-9672800	Weak transcription	HSMMtube	muscle
7	chr1:9654000-9673200	Weak transcription	NH-A	brain
8	chr1:9654000-9673800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:9654000-9675600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:9654400-9675400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:9655200-9666600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:9655400-9674200	Strong transcription	Dnd41	blood
13	chr1:9655600-9674200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:9655600-9674600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:9655800-9674000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:9655800-9674200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:9655800-9674800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:9656000-9674000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:9656400-9674000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:9656600-9666200	Strong transcription	Thymus	Thymus
21	chr1:9656800-9674200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:9656800-9674400	Strong transcription	Ovary	ovary
23	chr1:9656800-9674600	Weak transcription	HMEC	breast
24	chr1:9657000-9666200	Strong transcription	Brain Hippocampus Middle	brain
25	chr1:9657000-9673600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr1:9657200-9697600	Weak transcription	Right Atrium	heart
27	chr1:9657400-9672400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:9657600-9668200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:9658000-9666600	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:9658400-9668600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:9658800-9671800	Weak transcription	Small Intestine	intestine
32	chr1:9659800-9674200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:9659800-9674200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:9659800-9674200	Strong transcription	Lung	lung
35	chr1:9659800-9674200	Strong transcription	Spleen	Spleen
36	chr1:9659800-9674400	Strong transcription	Stomach Smooth Muscle	stomach
37	chr1:9660000-9666200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:9660200-9674000	Strong transcription	Adipose Nuclei	Adipose
39	chr1:9660200-9674000	Strong transcription	Fetal Intestine Large	intestine
40	chr1:9660200-9674200	Strong transcription	Placenta	Placenta
41	chr1:9660400-9673600	Strong transcription	Gastric	stomach
42	chr1:9660600-9676800	Weak transcription	HSMM	muscle
43	chr1:9662000-9668400	Weak transcription	GM12878-XiMat	blood
44	chr1:9662000-9675200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:9662000-9675800	Weak transcription	Primary B cells from cord blood	blood
46	chr1:9662200-9674200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:9662200-9676400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr1:9662400-9666600	Weak transcription	Psoas Muscle	Psoas
49	chr1:9662400-9667800	Weak transcription	HepG2	liver
50	chr1:9662400-9670000	Weak transcription	Muscle Satellite Cultured Cells	--

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