Variant report

Variant	rs13271797
Chromosome Location	chr8:8885954-8885955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10217044	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045527	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045528	1.00[CHD][hapmap]
rs1045529	0.89[CEU][hapmap]
rs11784393	0.81[CEU][hapmap]
rs11785634	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11785819	1.00[CEU][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11787026	0.87[ASW][hapmap];0.93[CEU][hapmap];0.93[LWK][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12114954	0.93[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13250919	1.00[CHD][hapmap]
rs13252797	1.00[CEU][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13273769	1.00[CHD][hapmap]
rs1562211	0.81[CEU][hapmap]
rs17702602	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2288671	0.85[CEU][hapmap]
rs2409120	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28482034	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28665409	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915251	0.85[CEU][hapmap]
rs2956244	0.88[CEU][hapmap]
rs2979247	0.85[CEU][hapmap]
rs2979256	0.85[CEU][hapmap]
rs2979265	0.85[CEU][hapmap]
rs34004903	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34251783	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3855900	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3895823	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3989373	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4840389	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4841083	0.92[CEU][hapmap]
rs4841088	1.00[CHD][hapmap]
rs6601279	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6601280	0.92[CEU][hapmap];0.81[LWK][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6601281	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6601282	0.81[CEU][hapmap]
rs6748	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.90[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6981060	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6983877	0.93[CEU][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6986044	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987107	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987558	0.85[CEU][hapmap]
rs7005056	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7005133	0.81[CEU][hapmap]
rs7017868	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7462373	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7814328	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9329175	0.96[CEU][hapmap];0.81[GIH][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9650616	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][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	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv831229	chr8:8751523-8926235	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv610205	chr8:8799111-8891644	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	n/a
5	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13271797	SGK223	cis	Thyroid	GTEx
rs13271797	THEX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8861200-8892400	Weak transcription	Aorta	Aorta
2	chr8:8861400-8907000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:8861800-8887200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr8:8861800-8887400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr8:8861800-8890000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr8:8861800-8891400	Weak transcription	Brain Angular Gyrus	brain
7	chr8:8861800-8891800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr8:8861800-8892000	Weak transcription	Brain Anterior Caudate	brain
9	chr8:8861800-8892200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr8:8861800-8892200	Weak transcription	Ovary	ovary
11	chr8:8861800-8893800	Weak transcription	Fetal Brain Male	brain
12	chr8:8861800-8897800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr8:8861800-8915600	Weak transcription	Pancreas	Pancrea
14	chr8:8865400-8886000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr8:8870600-8892200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr8:8871200-8900000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr8:8871400-8892800	Weak transcription	HSMMtube	muscle
18	chr8:8871800-8887200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr8:8871800-8894400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr8:8872000-8891200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr8:8872400-8887200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr8:8875000-8891200	Weak transcription	Fetal Intestine Small	intestine
23	chr8:8875200-8887200	Weak transcription	Brain Substantia Nigra	brain
24	chr8:8875200-8897200	Weak transcription	Gastric	stomach
25	chr8:8875400-8890200	Weak transcription	Fetal Stomach	stomach
26	chr8:8875400-8892600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr8:8875400-8894400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr8:8875400-8897000	Weak transcription	Lung	lung
29	chr8:8875400-8901200	Weak transcription	Thymus	Thymus
30	chr8:8875600-8886000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr8:8875600-8890000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr8:8875600-8890200	Weak transcription	HSMM	muscle
33	chr8:8875800-8892200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr8:8876400-8887200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr8:8876400-8890000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr8:8876400-8898000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr8:8876800-8890000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr8:8876800-8891400	Weak transcription	Fetal Brain Female	brain
39	chr8:8877000-8894600	Weak transcription	HMEC	breast
40	chr8:8877000-8895600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr8:8877000-8903400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr8:8877200-8895400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr8:8878600-8890200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr8:8878800-8890200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr8:8879000-8890000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr8:8879200-8892600	Weak transcription	Osteobl	bone
47	chr8:8879400-8894200	Weak transcription	HepG2	liver
48	chr8:8879600-8887200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr8:8880000-8890000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr8:8880600-8890200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links