Variant report

Variant	rs12866447
Chromosome Location	chr13:50316352-50316353
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1061979	0.96[GIH][hapmap];1.00[YRI][hapmap]
rs11148161	0.85[CEU][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11148164	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs11148167	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12428108	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12430539	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12584401	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12584560	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12864534	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12868235	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12869900	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12875005	0.81[EUR][1000 genomes]
rs12876223	0.81[CEU][hapmap];0.94[EUR][1000 genomes]
rs12876889	0.81[EUR][1000 genomes]
rs12877931	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1535543	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1575387	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1581744	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1923730	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];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146143	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2236354	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34423763	0.81[EUR][1000 genomes]
rs35331571	0.86[EUR][1000 genomes]
rs35672544	0.84[AMR][1000 genomes]
rs3742095	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4603448	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4643206	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4941657	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4942864	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942870	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6561552	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs71428292	0.81[EUR][1000 genomes]
rs73194404	0.91[ASN][1000 genomes]
rs7329488	0.96[GIH][hapmap];1.00[YRI][hapmap]
rs7446	1.00[ASW][hapmap];0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7987502	0.86[CEU][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7997798	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9526586	0.82[YRI][hapmap]
rs9526592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9526595	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526600	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535294	0.93[GIH][hapmap];1.00[YRI][hapmap]
rs9535301	1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs9535315	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9535326	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];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535332	0.86[CEU][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535337	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9535339	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535344	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9535345	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9535347	1.00[ASW][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9535352	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9535356	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9646001	0.86[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900072	chr13:50266109-50381016	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv900073	chr13:50286218-50381016	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv1818134	chr13:50306897-50374102	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12866447	EBPL	Cis_1M	lymphoblastoid	RTeQTL
rs12866447	KPNA3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
2	chr13:50273200-50326000	Weak transcription	Aorta	Aorta
3	chr13:50273200-50333800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:50277000-50318400	Weak transcription	Hela-S3	cervix
5	chr13:50290000-50324000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr13:50290000-50334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr13:50290200-50316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr13:50293200-50326000	Weak transcription	Fetal Brain Male	brain
9	chr13:50294200-50324000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr13:50294400-50333000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr13:50296200-50330400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr13:50296400-50320200	Weak transcription	Spleen	Spleen
13	chr13:50296600-50330400	Weak transcription	Small Intestine	intestine
14	chr13:50296600-50338600	Weak transcription	Ovary	ovary
15	chr13:50297000-50322400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr13:50298000-50327600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:50299200-50327600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr13:50299400-50319400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr13:50300600-50345600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr13:50300800-50321800	Weak transcription	Brain Anterior Caudate	brain
21	chr13:50301000-50319200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr13:50301200-50323600	Weak transcription	Colon Smooth Muscle	Colon
23	chr13:50301200-50327800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr13:50302800-50333800	Weak transcription	Thymus	Thymus
25	chr13:50303200-50319400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr13:50303200-50334000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr13:50304400-50321400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr13:50305600-50319400	Weak transcription	Fetal Intestine Small	intestine
29	chr13:50305600-50319600	Weak transcription	Fetal Stomach	stomach
30	chr13:50305800-50319400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr13:50305800-50320200	Weak transcription	Fetal Muscle Leg	muscle
32	chr13:50306000-50316600	Weak transcription	Fetal Intestine Large	intestine
33	chr13:50306000-50318400	Weak transcription	Placenta	Placenta
34	chr13:50306000-50319000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr13:50306000-50320200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr13:50306000-50324000	Weak transcription	HSMMtube	muscle
37	chr13:50306000-50351600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr13:50306200-50323200	Weak transcription	Brain Germinal Matrix	brain
39	chr13:50306200-50334200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr13:50306200-50336200	Weak transcription	Adipose Nuclei	Adipose
41	chr13:50306600-50316800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr13:50306600-50318200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr13:50306600-50319000	Weak transcription	Osteobl	bone
44	chr13:50306600-50323200	Weak transcription	NHEK	skin
45	chr13:50306800-50316600	Weak transcription	NHDF-Ad	bronchial
46	chr13:50306800-50317200	Weak transcription	Fetal Thymus	thymus
47	chr13:50306800-50317800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr13:50306800-50318000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr13:50306800-50318000	Weak transcription	HUVEC	blood vessel
50	chr13:50306800-50319000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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