Variant report

Variant	rs59816011
Chromosome Location	chr3:67637945-67637946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:67626314..67629227-chr3:67636253..67638089,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1028950	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11711916	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12485966	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488912	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1576398	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1590875	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17808406	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1974109	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2078020	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2634725	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2634729	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2634735	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4856878	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56033013	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56157830	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56193099	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57578558	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59116776	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60923125	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256409	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6780493	0.81[ASN][1000 genomes]
rs6797488	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[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	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
2	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
3	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
4	nsv590561	chr3:67548852-67690626	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv3359258	chr3:67589615-67828274	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv275108	chr3:67633420-67640906	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv876922	chr3:67635506-67755257	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59816011	SUCLG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67579400-67657600	Weak transcription	Pancreas	Pancrea
2	chr3:67595000-67639400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:67598000-67644200	Weak transcription	NHLF	lung
4	chr3:67601800-67673000	Weak transcription	Fetal Heart	heart
5	chr3:67602200-67644200	Weak transcription	Gastric	stomach
6	chr3:67602200-67654800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:67602200-67655400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:67602200-67656000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:67602400-67646200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:67609400-67644000	Weak transcription	NHDF-Ad	bronchial
11	chr3:67612400-67697200	Weak transcription	Hela-S3	cervix
12	chr3:67614000-67658600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:67616600-67644200	Weak transcription	HSMM	muscle
14	chr3:67618600-67655600	Weak transcription	NH-A	brain
15	chr3:67620400-67639800	Weak transcription	Small Intestine	intestine
16	chr3:67621200-67644200	Weak transcription	Esophagus	oesophagus
17	chr3:67621200-67657600	Weak transcription	Fetal Stomach	stomach
18	chr3:67621400-67640000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:67621400-67650400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:67621800-67639400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:67621800-67640600	Weak transcription	Placenta	Placenta
22	chr3:67621800-67644000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:67621800-67658000	Weak transcription	Thymus	Thymus
24	chr3:67622000-67640800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr3:67622000-67641400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr3:67622000-67648800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:67622200-67657400	Weak transcription	Brain Substantia Nigra	brain
28	chr3:67622400-67647800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:67622600-67644400	Weak transcription	HMEC	breast
30	chr3:67622800-67644000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:67623400-67650000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:67624400-67643800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:67624400-67649200	Weak transcription	Fetal Intestine Large	intestine
34	chr3:67624800-67643800	Weak transcription	Dnd41	blood
35	chr3:67624800-67649200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:67624800-67651000	Weak transcription	Adipose Nuclei	Adipose
37	chr3:67624800-67658200	Weak transcription	Fetal Intestine Small	intestine
38	chr3:67627200-67655400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:67627600-67649000	Weak transcription	NHEK	skin
40	chr3:67628400-67655000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:67629200-67654800	Weak transcription	Fetal Kidney	kidney
42	chr3:67629200-67675000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:67629400-67639400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:67629400-67639400	Weak transcription	Lung	lung
45	chr3:67629400-67644000	Weak transcription	Right Atrium	heart
46	chr3:67629400-67645600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:67629400-67648800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:67629400-67649200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:67629400-67649400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:67629400-67658000	Weak transcription	Right Ventricle	heart

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