Variant report

Variant	rs2190342
Chromosome Location	chr7:41049998-41049999
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11771067	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12113729	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12701858	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13222733	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13235016	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs13239481	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13247967	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1548630	0.83[ASN][1000 genomes]
rs17622437	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1859699	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1990137	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1990138	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2108183	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35274819	0.91[EUR][1000 genomes]
rs4329187	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4454200	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59555466	0.84[ASN][1000 genomes]
rs6959994	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs6960159	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs6974297	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs757913	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7776627	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7783070	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7792912	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7800626	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9769724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs979863	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv5714	chr7:41026022-41059813	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2190342	TMED4	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:41037000-41050400	Weak transcription	Aorta	Aorta
2	chr7:41042200-41050600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:41046400-41050000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:41046400-41050000	Weak transcription	Adipose Nuclei	Adipose
5	chr7:41047200-41050000	Weak transcription	NHLF	lung
6	chr7:41047200-41050200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:41047200-41050200	Weak transcription	HUVEC	blood vessel
8	chr7:41047400-41050000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:41047400-41050200	Weak transcription	HSMMtube	muscle
10	chr7:41047800-41050000	Weak transcription	HSMM	muscle
11	chr7:41047800-41050400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:41047800-41052800	Weak transcription	NH-A	brain
13	chr7:41048000-41050400	Weak transcription	Osteobl	bone
14	chr7:41048000-41051400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:41048200-41050000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr7:41048400-41050000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:41048400-41050400	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr7:41048600-41065600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:41049000-41051600	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr7:41049200-41052000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr7:41049600-41051600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:41049600-41052000	Enhancers	Fetal Muscle Leg	muscle
23	chr7:41049800-41050200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr7:41049800-41050800	Enhancers	Hela-S3	cervix
25	chr7:41049800-41051600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr7:41049800-41051800	Enhancers	NHDF-Ad	bronchial
27	chr7:41049800-41053200	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links