Variant report

Variant	rs13561
Chromosome Location	chr12:106903321-106903322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:106868319..106871303-chr12:106901401..106903700,2	K562	blood:
2	chr12:106900457..106902136-chr12:106902271..106904161,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10778483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778484	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861600	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10861607	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10861615	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861616	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112983	0.81[EUR][1000 genomes]
rs11113012	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11113014	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11113015	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11113016	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11113020	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11113023	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11113025	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12231768	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17038484	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1882413	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2243506	1.00[ASW][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap]
rs2245062	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2246353	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2249162	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2249773	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs2250262	0.86[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.82[AMR][1000 genomes]
rs2252685	0.86[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs2253054	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2288266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288269	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2374609	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34619628	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3851635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3902141	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964460	0.82[MEX][hapmap]
rs741624	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3435035	chr12:106765277-107015325	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832510	chr12:106787730-106951140	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13561	POLR3B	cis	multi-tissue	Pritchard
rs13561	TCP11L2	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106828600-106905800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:106854400-106904800	Weak transcription	HSMM	muscle
3	chr12:106886200-106916400	Weak transcription	A549	lung
4	chr12:106887600-106907800	Weak transcription	Small Intestine	intestine
5	chr12:106888200-106906800	Weak transcription	Brain Substantia Nigra	brain
6	chr12:106889200-106904600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr12:106889200-106905400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:106889400-106904000	Strong transcription	Primary T cells from cord blood	blood
9	chr12:106889400-106904600	Strong transcription	Liver	Liver
10	chr12:106890000-106904200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr12:106890800-106905200	Weak transcription	Colonic Mucosa	Colon
12	chr12:106892000-106904400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:106892000-106905200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:106892000-106906400	Weak transcription	Brain Angular Gyrus	brain
15	chr12:106892000-106907800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:106892400-106905200	Weak transcription	NHEK	skin
17	chr12:106892800-106904000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:106892800-106905600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:106894400-106916400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:106894600-106905200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:106894600-106913200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:106895600-106904000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:106896400-106906600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:106896400-106906800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:106896400-106907200	Weak transcription	Esophagus	oesophagus
26	chr12:106896400-106908400	Weak transcription	NHLF	lung
27	chr12:106896400-106916800	Weak transcription	Fetal Intestine Small	intestine
28	chr12:106896600-106905200	Weak transcription	Fetal Heart	heart
29	chr12:106896600-106906400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:106897000-106905000	Weak transcription	Right Atrium	heart
31	chr12:106897400-106905600	Strong transcription	Placenta	Placenta
32	chr12:106897800-106904000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:106898200-106905000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:106898200-106907600	Weak transcription	K562	blood
35	chr12:106898600-106903400	Weak transcription	Primary B cells from cord blood	blood
36	chr12:106898600-106904600	Weak transcription	Pancreas	Pancrea
37	chr12:106898600-106905400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:106898600-106906600	Weak transcription	Fetal Brain Female	brain
39	chr12:106898600-106906800	Weak transcription	Osteobl	bone
40	chr12:106898600-106916000	Weak transcription	HepG2	liver
41	chr12:106898800-106904400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:106898800-106904800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:106898800-106905600	Weak transcription	Fetal Intestine Large	intestine
44	chr12:106898800-106905600	Weak transcription	HSMMtube	muscle
45	chr12:106898800-106913200	Weak transcription	Fetal Lung	lung
46	chr12:106899000-106905400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr12:106899000-106906000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:106899000-106907000	Weak transcription	Gastric	stomach
49	chr12:106899200-106905400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr12:106899200-106907000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links