Variant report

Variant	rs9812544
Chromosome Location	chr3:191117867-191117868
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10513865	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1369278	0.89[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs1369279	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs1474188	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16822368	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16822380	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16822451	0.97[ASN][1000 genomes]
rs16848976	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs16866501	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs16866503	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs16866506	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs1715641	0.83[CHB][hapmap]
rs17811727	0.83[TSI][hapmap]
rs2117548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2293379	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28502671	0.86[AFR][1000 genomes]
rs293810	0.83[CHD][hapmap]
rs293840	0.84[CHD][hapmap]
rs420266	0.84[CHD][hapmap]
rs4247189	0.80[ASN][1000 genomes]
rs4247190	0.89[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs436393	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs438589	0.84[CHD][hapmap]
rs4677633	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4677731	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs57369465	0.80[ASN][1000 genomes]
rs57831251	0.80[ASN][1000 genomes]
rs58077600	0.86[ASN][1000 genomes]
rs58596458	0.80[ASN][1000 genomes]
rs58631024	0.97[ASN][1000 genomes]
rs58648691	0.97[ASN][1000 genomes]
rs59491001	0.99[ASN][1000 genomes]
rs60089463	0.97[ASN][1000 genomes]
rs60176909	0.99[ASN][1000 genomes]
rs60204557	0.86[ASN][1000 genomes]
rs9827142	0.86[AFR][1000 genomes]
rs9832656	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9838800	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9839989	0.80[AFR][1000 genomes]
rs9844500	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9854318	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9854581	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9868286	0.82[ASW][hapmap];0.82[LWK][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9812544	CCDC50	cis	Esophagus Muscularis	GTEx
rs9812544	CCDC50	cis	Artery Tibial	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191079600-191121200	Weak transcription	Gastric	stomach
2	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
3	chr3:191088600-191119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:191093400-191119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
6	chr3:191096000-191130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:191099400-191122000	Weak transcription	Fetal Brain Male	brain
8	chr3:191099600-191120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:191100200-191119200	Weak transcription	Right Ventricle	heart
10	chr3:191100200-191119400	Weak transcription	Psoas Muscle	Psoas
11	chr3:191100200-191119600	Weak transcription	K562	blood
12	chr3:191100400-191120000	Weak transcription	Spleen	Spleen
13	chr3:191100400-191121600	Weak transcription	Fetal Brain Female	brain
14	chr3:191103200-191119400	Weak transcription	HSMMtube	muscle
15	chr3:191108600-191118000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:191108600-191118800	Weak transcription	Brain Germinal Matrix	brain
17	chr3:191108800-191119400	Weak transcription	Aorta	Aorta
18	chr3:191110400-191118000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:191110800-191119400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:191111000-191130400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:191111200-191118000	Weak transcription	Fetal Lung	lung
22	chr3:191112000-191118000	Strong transcription	Adipose Nuclei	Adipose
23	chr3:191112200-191118400	Strong transcription	NH-A	brain
24	chr3:191113200-191118200	Weak transcription	Hela-S3	cervix
25	chr3:191113600-191118200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:191114000-191121400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:191114200-191118000	Weak transcription	NHDF-Ad	bronchial
28	chr3:191114200-191119200	Weak transcription	Fetal Intestine Large	intestine
29	chr3:191114200-191119400	Weak transcription	NHLF	lung
30	chr3:191114400-191119600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:191114400-191119600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:191114400-191120400	Weak transcription	HSMM	muscle
33	chr3:191114400-191121000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:191114400-191121400	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:191114600-191118200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:191115400-191118000	Strong transcription	HUVEC	blood vessel
37	chr3:191115400-191118200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:191116000-191119800	Weak transcription	Left Ventricle	heart
39	chr3:191116000-191119800	Weak transcription	Ovary	ovary
40	chr3:191116000-191121200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:191116000-191121600	Weak transcription	Primary B cells from cord blood	blood
42	chr3:191116400-191118800	Weak transcription	Placenta	Placenta
43	chr3:191116600-191118400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:191116600-191118800	Weak transcription	Osteobl	bone
45	chr3:191116600-191119600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:191116600-191119600	Weak transcription	Liver	Liver
47	chr3:191117000-191118600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr3:191117000-191118600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr3:191117200-191127200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:191117200-191127200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links