Variant report

Variant	rs12613489
Chromosome Location	chr2:182172593-182172594
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	chr2:182169769-182172732	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:182169768-182172686	GM12891	blood:	n/a	n/a
3	POLR2A	chr2:182168803-182172708	GM18505	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:182169176..182171895-chr2:182171917..182174599,2	K562	blood:

Variant related genes	Relation type
MIR4437	TF binding region
ENSG00000266705	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10178445	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10183522	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10497578	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12621029	0.81[EUR][1000 genomes]
rs12621069	0.81[EUR][1000 genomes]
rs12623733	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16823661	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16867395	0.81[EUR][1000 genomes]
rs16867396	0.81[EUR][1000 genomes]
rs16867398	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16867399	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16867403	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16867404	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16867407	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16867409	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16867411	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16867412	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16867414	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16867415	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16867417	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16867418	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16867421	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4627521	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58869569	0.81[EUR][1000 genomes]
rs60453369	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60481141	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61097715	0.80[EUR][1000 genomes];0.87[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	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1002647	chr2:182078521-182392273	Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv536064	chr2:182078521-182392273	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182168400-182174000	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr2:182168600-182174000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:182168600-182174200	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:182168600-182176800	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr2:182168800-182174200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:182170600-182173000	Weak transcription	Small Intestine	intestine
7	chr2:182170800-182173200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:182170800-182173400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:182171000-182173000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:182171000-182173200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr2:182171000-182173400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr2:182171200-182173400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:182171400-182173000	Weak transcription	Adipose Nuclei	Adipose
14	chr2:182171400-182174000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:182171600-182172800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:182171600-182173200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:182172000-182174000	Enhancers	Primary hematopoietic stem cells	blood
18	chr2:182172200-182172600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr2:182172200-182173000	Enhancers	Primary T cells from cord blood	blood
20	chr2:182172200-182173200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr2:182172200-182173200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr2:182172200-182173200	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr2:182172200-182173200	Enhancers	Dnd41	blood
24	chr2:182172200-182173200	Enhancers	GM12878-XiMat	blood
25	chr2:182172200-182173200	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr2:182172200-182173400	Enhancers	Primary B cells from cord blood	blood
27	chr2:182172200-182173400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:182172200-182173400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr2:182172200-182174000	Enhancers	Primary T cells fromperipheralblood	blood
30	chr2:182172200-182174000	Enhancers	Fetal Thymus	thymus
31	chr2:182172200-182176200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr2:182172200-182178000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:182172200-182179000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:182172400-182172800	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr2:182172400-182172800	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links