Variant report

Variant	rs13269739
Chromosome Location	chr8:86054252-86054253
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10088120	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10090196	0.86[JPT][hapmap]
rs10091577	0.90[ASN][1000 genomes]
rs10091710	0.89[ASN][1000 genomes]
rs10100442	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10104630	0.90[JPT][hapmap]
rs1021583	0.95[JPT][hapmap]
rs11261468	0.90[JPT][hapmap]
rs11261471	0.90[JPT][hapmap]
rs12541445	0.90[JPT][hapmap]
rs12543256	0.95[JPT][hapmap]
rs12546106	0.95[JPT][hapmap]
rs12549421	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12550160	0.95[JPT][hapmap]
rs12926	0.86[ASN][1000 genomes]
rs1303806	0.82[JPT][hapmap]
rs13249364	0.90[ASN][1000 genomes]
rs13259399	0.86[JPT][hapmap]
rs13269031	0.90[ASN][1000 genomes]
rs1390711	0.82[JPT][hapmap]
rs1496531	0.86[JPT][hapmap]
rs1496532	0.86[JPT][hapmap]
rs1553015	0.82[JPT][hapmap]
rs16913681	0.95[JPT][hapmap]
rs16913721	0.86[JPT][hapmap]
rs17740658	0.95[JPT][hapmap]
rs1908762	0.90[JPT][hapmap]
rs1995057	0.90[JPT][hapmap];0.84[TSI][hapmap]
rs1995058	0.82[JPT][hapmap];0.82[TSI][hapmap]
rs2006767	0.86[JPT][hapmap]
rs2088305	1.00[YRI][hapmap]
rs2132589	0.95[JPT][hapmap]
rs2278459	0.90[JPT][hapmap]
rs2279701	0.90[JPT][hapmap]
rs2291786	0.95[JPT][hapmap]
rs2291787	0.90[JPT][hapmap];0.82[TSI][hapmap]
rs2403083	1.00[JPT][hapmap]
rs2403085	1.00[JPT][hapmap]
rs2403086	1.00[JPT][hapmap]
rs2403088	0.90[JPT][hapmap]
rs2403104	0.81[JPT][hapmap]
rs28621707	0.87[ASN][1000 genomes]
rs2896452	0.90[JPT][hapmap]
rs2896454	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs34103685	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs34527380	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3779899	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3779901	0.95[JPT][hapmap]
rs3808538	0.86[JPT][hapmap]
rs3808539	0.82[JPT][hapmap]
rs4150859	0.87[ASN][1000 genomes]
rs4150865	0.87[ASN][1000 genomes]
rs4150867	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4150868	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4150869	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4150884	0.87[ASN][1000 genomes]
rs4150893	1.00[JPT][hapmap]
rs4150909	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4150942	0.90[JPT][hapmap]
rs4150944	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4150964	0.95[JPT][hapmap]
rs4150974	0.95[JPT][hapmap]
rs4150977	0.95[JPT][hapmap]
rs4609189	0.95[JPT][hapmap]
rs4739700	0.86[JPT][hapmap]
rs4740043	0.85[JPT][hapmap]
rs4740044	0.86[JPT][hapmap]
rs4740045	0.95[JPT][hapmap]
rs4740049	0.82[JPT][hapmap]
rs62527168	0.89[ASN][1000 genomes]
rs62527173	0.90[ASN][1000 genomes]
rs6605610	0.95[JPT][hapmap]
rs6605611	0.95[JPT][hapmap]
rs6605624	0.90[JPT][hapmap]
rs6990449	0.86[JPT][hapmap]
rs6993387	0.86[JPT][hapmap]
rs6994113	0.95[JPT][hapmap]
rs7001359	0.90[JPT][hapmap]
rs7004765	0.92[ASN][1000 genomes]
rs7008032	0.88[ASN][1000 genomes]
rs7008772	0.86[JPT][hapmap]
rs7010228	0.87[ASN][1000 genomes]
rs7011926	0.82[JPT][hapmap]
rs7015758	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7818163	0.86[JPT][hapmap]
rs7823218	0.89[ASN][1000 genomes]
rs7826589	0.85[JPT][hapmap]
rs7827175	0.95[JPT][hapmap]
rs7829050	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7829144	0.90[JPT][hapmap]
rs7841142	0.90[JPT][hapmap]
rs7842013	0.90[ASN][1000 genomes]
rs903895	0.82[JPT][hapmap];0.82[TSI][hapmap]
rs903896	0.82[JPT][hapmap]
rs903897	0.82[JPT][hapmap]
rs9692962	0.90[JPT][hapmap]

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	esv3481417	chr8:85279453-86145229	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3481418	chr8:85279453-86145229	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1797206	chr8:86023237-86060072	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	esv1800945	chr8:86030101-86060072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13269739	CA2	cis	lymphoblastoid	seeQTL
rs13269739	LRRCC1	cis	Esophagus Mucosa	GTEx
rs13269739	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs13269739	C8orf59	cis	cerebellum	SCAN
rs13269739	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs13269739	CA13	cis	cerebellum	SCAN
rs13269739	C8orf59	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86020000-86057400	Weak transcription	Small Intestine	intestine
2	chr8:86020400-86054800	Weak transcription	Lung	lung
3	chr8:86020400-86055400	Weak transcription	Fetal Kidney	kidney
4	chr8:86020400-86055400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr8:86020400-86056400	Weak transcription	Gastric	stomach
6	chr8:86020400-86057400	Weak transcription	Aorta	Aorta
7	chr8:86020400-86062600	Weak transcription	Pancreas	Pancrea
8	chr8:86020600-86054600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr8:86020600-86058800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr8:86021200-86058800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr8:86021200-86059600	Weak transcription	Fetal Brain Male	brain
12	chr8:86021400-86058400	Weak transcription	Brain Germinal Matrix	brain
13	chr8:86025200-86057400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr8:86028400-86059000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr8:86028600-86056400	Weak transcription	Ovary	ovary
16	chr8:86032800-86057400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr8:86033000-86059800	Weak transcription	Fetal Thymus	thymus
18	chr8:86035200-86055600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr8:86037000-86061200	Weak transcription	Brain Anterior Caudate	brain
20	chr8:86037400-86056000	Weak transcription	Right Ventricle	heart
21	chr8:86038000-86057200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr8:86038800-86057400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr8:86039400-86056200	Weak transcription	Brain Hippocampus Middle	brain
24	chr8:86039600-86058400	Weak transcription	Esophagus	oesophagus
25	chr8:86040200-86056600	Weak transcription	Fetal Brain Female	brain
26	chr8:86040600-86062000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr8:86043000-86058800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr8:86043200-86057200	Weak transcription	Left Ventricle	heart
29	chr8:86044200-86060000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr8:86044400-86056200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr8:86045600-86056400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr8:86045600-86057200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr8:86046200-86055600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr8:86046600-86055000	Weak transcription	Colon Smooth Muscle	Colon
35	chr8:86046600-86064800	Weak transcription	Thymus	Thymus
36	chr8:86046600-86065800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr8:86048800-86059000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr8:86049000-86055000	Strong transcription	Dnd41	blood
39	chr8:86049400-86056200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr8:86049400-86056400	Weak transcription	Fetal Muscle Leg	muscle
41	chr8:86049400-86057400	Weak transcription	Fetal Intestine Large	intestine
42	chr8:86049400-86065800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr8:86050200-86055800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr8:86050800-86056200	Weak transcription	HMEC	breast
45	chr8:86050800-86061400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr8:86051000-86056800	Weak transcription	Fetal Lung	lung
47	chr8:86051000-86057200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr8:86051000-86057400	Weak transcription	Adipose Nuclei	Adipose
49	chr8:86051000-86057600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr8:86051000-86059800	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links