Variant report

Variant	rs7953579
Chromosome Location	chr12:21807687-21807688
allele	C/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	SP1	chr12:21807381-21807703	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:21806858-21807893	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr12:21807285-21808189	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr12:21807636-21808167	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:21807374-21808271	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr12:21807381-21808162	GM12892	blood:	n/a	n/a
7	POLR2A	chr12:21807648-21807793	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr12:21806376-21807725	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr12:21794854-21807737	K562	blood:	n/a	n/a
10	POLR2A	chr12:21805104-21807913	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr12:21807686-21807715	K562	blood:	n/a	n/a
12	POLR2A	chr12:21805185-21809496	A549	lung:	n/a	n/a
13	POLR2A	chr12:21807385-21807762	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr12:21807342-21808125	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
LDHB	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10770848	0.82[CHB][hapmap]
rs10841860	0.80[ASN][1000 genomes]
rs10841862	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10841867	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10841868	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10841869	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10841872	0.85[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs10841873	0.81[ASN][1000 genomes]
rs10841874	0.85[ASN][1000 genomes]
rs11046147	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11046148	0.86[ASN][1000 genomes]
rs11046149	0.88[ASN][1000 genomes]
rs11046150	0.88[ASN][1000 genomes]
rs11046151	0.82[ASN][1000 genomes]
rs11046153	0.85[ASN][1000 genomes]
rs11046154	0.85[ASN][1000 genomes]
rs11046156	0.85[ASN][1000 genomes]
rs11046157	0.83[CHB][hapmap]
rs11046159	0.82[CHB][hapmap]
rs11046160	0.80[CHB][hapmap]
rs11836830	0.86[ASN][1000 genomes]
rs12824571	0.88[ASN][1000 genomes]
rs12824788	0.86[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12824936	0.84[ASN][1000 genomes]
rs12825320	0.88[ASN][1000 genomes]
rs12826014	0.84[ASN][1000 genomes]
rs12829701	0.88[ASN][1000 genomes]
rs12830306	0.88[ASN][1000 genomes]
rs1478290	0.82[CHB][hapmap]
rs153941	0.91[CHB][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs1650307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1677084	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1677091	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1677137	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs192210	0.81[CHB][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs1981948	0.83[CHB][hapmap]
rs255447	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4762855	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58134911	0.85[ASN][1000 genomes]
rs60462572	0.86[ASN][1000 genomes]
rs66978947	0.88[ASN][1000 genomes]
rs67247140	0.83[ASN][1000 genomes]
rs67286733	0.86[ASN][1000 genomes]
rs7133519	0.82[CHB][hapmap]
rs7135965	0.86[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7297042	0.85[ASN][1000 genomes]
rs7301883	0.82[CHB][hapmap]
rs7302534	0.88[ASN][1000 genomes]
rs7302639	0.88[ASN][1000 genomes]
rs7303185	0.88[ASN][1000 genomes]
rs7303528	0.85[ASN][1000 genomes]
rs7303612	0.88[ASN][1000 genomes]
rs7303644	0.85[ASN][1000 genomes]
rs73077300	0.86[ASN][1000 genomes]
rs7316669	0.82[CHB][hapmap]

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	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv469164	chr12:21688900-21966701	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv557744	chr12:21688900-21966701	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv832349	chr12:21749093-21930695	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7953579	RP11-59N23.3	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21781200-21809600	Weak transcription	Small Intestine	intestine
2	chr12:21786400-21807800	Strong transcription	Osteobl	bone
3	chr12:21787000-21807800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:21787000-21807800	Strong transcription	Primary hematopoietic stem cells	blood
5	chr12:21787200-21808200	Strong transcription	NH-A	brain
6	chr12:21787200-21808600	Strong transcription	HMEC	breast
7	chr12:21787200-21808600	Strong transcription	HSMM	muscle
8	chr12:21788000-21809200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:21788600-21810000	Weak transcription	Liver	Liver
10	chr12:21790000-21808200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr12:21791800-21809400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:21793200-21807800	Strong transcription	Fetal Thymus	thymus
13	chr12:21793600-21808000	Strong transcription	Fetal Muscle Leg	muscle
14	chr12:21796600-21807800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:21798600-21808000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:21798800-21808000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:21798800-21808000	Strong transcription	NHLF	lung
18	chr12:21798800-21809600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:21799000-21807800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:21799000-21808200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:21799200-21807800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:21799200-21808400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:21799400-21808200	Strong transcription	NHEK	skin
24	chr12:21799600-21807800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:21800000-21808400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:21801200-21807800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
27	chr12:21802000-21808200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr12:21803600-21808000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:21803800-21808000	Genic enhancers	Primary T cells fromperipheralblood	blood
30	chr12:21803800-21808000	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:21803800-21808000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:21804000-21807800	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr12:21804000-21809200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:21804200-21808000	Weak transcription	Right Atrium	heart
35	chr12:21804200-21810000	Weak transcription	Stomach Mucosa	stomach
36	chr12:21804400-21809200	Weak transcription	Fetal Stomach	stomach
37	chr12:21804400-21810000	Weak transcription	Spleen	Spleen
38	chr12:21804600-21808000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr12:21804600-21808800	Weak transcription	Fetal Intestine Small	intestine
40	chr12:21804600-21809000	Weak transcription	Brain Germinal Matrix	brain
41	chr12:21804600-21809600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr12:21804600-21809800	Weak transcription	Esophagus	oesophagus
43	chr12:21804600-21809800	Weak transcription	Gastric	stomach
44	chr12:21805200-21807800	Genic enhancers	Brain Substantia Nigra	brain
45	chr12:21805200-21808600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:21805400-21807800	Strong transcription	Fetal Lung	lung
47	chr12:21805800-21809000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:21806000-21807800	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr12:21806000-21808000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:21806000-21808000	Strong transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links