Variant report

Variant	rs11705861
Chromosome Location	chr3:67529166-67529167
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11127623	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11709258	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11920877	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11923553	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12374036	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12635531	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4327406	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4349513	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4645146	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56393250	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57077433	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60806282	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62256386	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62256387	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62256391	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256392	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62256395	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62256396	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62256399	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6779086	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6789939	0.85[EUR][1000 genomes]
rs6802566	0.85[EUR][1000 genomes]
rs6805028	0.85[EUR][1000 genomes]
rs6810165	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088910	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7429940	0.81[EUR][1000 genomes]
rs7630024	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7651649	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9873407	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007093	chr3:67113534-67602973	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS 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 target site	10 gene(s)	inside rSNPs	diseases
4	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv834719	chr3:67396626-67589852	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11705861	SUCLG2	cis	multi-tissue	Pritchard

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67435600-67534200	Weak transcription	Aorta	Aorta
2	chr3:67473600-67542000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:67482800-67533400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:67488000-67544200	Weak transcription	A549	lung
5	chr3:67488400-67566400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:67492200-67545400	Weak transcription	Fetal Intestine Small	intestine
7	chr3:67498000-67534200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:67500800-67567000	Weak transcription	Pancreas	Pancrea
9	chr3:67501200-67533600	Weak transcription	Fetal Intestine Large	intestine
10	chr3:67504000-67559800	Weak transcription	Esophagus	oesophagus
11	chr3:67506600-67544000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:67508200-67577600	Weak transcription	Spleen	Spleen
13	chr3:67508800-67542000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:67509000-67537200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:67509200-67534400	Weak transcription	Left Ventricle	heart
16	chr3:67511600-67560000	Weak transcription	Lung	lung
17	chr3:67511800-67565000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:67512200-67544000	Weak transcription	Adipose Nuclei	Adipose
19	chr3:67512200-67545200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:67512400-67534200	Weak transcription	Gastric	stomach
21	chr3:67512800-67537200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:67512800-67542400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:67512800-67544000	Weak transcription	Dnd41	blood
24	chr3:67512800-67544800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:67512800-67554800	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:67513000-67530800	Weak transcription	Fetal Stomach	stomach
27	chr3:67513200-67544000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr3:67513200-67544600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:67513200-67545200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:67513200-67564800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:67513400-67542600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:67513400-67567800	Weak transcription	NHLF	lung
33	chr3:67513600-67544200	Weak transcription	Liver	Liver
34	chr3:67513600-67559800	Weak transcription	NHDF-Ad	bronchial
35	chr3:67514400-67534000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:67514600-67559800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr3:67514800-67531200	Weak transcription	Ovary	ovary
38	chr3:67516200-67545000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:67517200-67529400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:67517400-67536800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:67517600-67542400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:67518800-67537000	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:67519000-67534000	Weak transcription	HSMM	muscle
44	chr3:67519000-67539200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:67519200-67545600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:67519400-67533400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr3:67519600-67533000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:67519600-67534400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:67519600-67541200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:67519800-67557400	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links