Variant report

Variant	rs7958198
Chromosome Location	chr12:59470536-59470537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10506354	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10735877	0.90[GIH][hapmap];0.88[TSI][hapmap]
rs10783935	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877204	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1444098	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1822586	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1967546	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2197332	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2197333	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2203085	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2218412	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2218413	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2371977	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2371978	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581229	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6650225	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7138934	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs894906	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs978615	0.81[EUR][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	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1047257	chr12:59444966-59520330	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1050662	chr12:59444966-59526442	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7958198	RDH16	cis	parietal	SCAN
rs7958198	MARCH9	cis	parietal	SCAN
rs7958198	OR6C74	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59454400-59471200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:59465800-59478000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:59466200-59471400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:59466400-59471000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:59468200-59470600	Enhancers	HUVEC	blood vessel
6	chr12:59468400-59489000	Weak transcription	Esophagus	oesophagus
7	chr12:59468600-59473000	Enhancers	Fetal Lung	lung
8	chr12:59468800-59471600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:59468800-59474200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr12:59469000-59472800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:59469400-59470800	Weak transcription	Fetal Stomach	stomach
12	chr12:59469400-59471800	Weak transcription	Small Intestine	intestine
13	chr12:59469600-59471800	Weak transcription	Gastric	stomach
14	chr12:59469600-59472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:59469800-59471400	Weak transcription	Fetal Muscle Leg	muscle
16	chr12:59470000-59470800	Enhancers	Osteobl	bone
17	chr12:59470000-59471000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:59470000-59471400	Enhancers	NHEK	skin
19	chr12:59470000-59471600	Enhancers	HMEC	breast
20	chr12:59470000-59472800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:59470000-59474400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:59470200-59471600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:59470200-59474400	Enhancers	Stomach Mucosa	stomach
24	chr12:59470400-59470600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:59470400-59470800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:59470400-59471000	Enhancers	NH-A	brain
27	chr12:59470400-59472000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:59470400-59472000	Enhancers	Fetal Intestine Large	intestine
29	chr12:59470400-59472000	Enhancers	Fetal Kidney	kidney
30	chr12:59470400-59472400	Enhancers	Fetal Intestine Small	intestine
31	chr12:59470400-59472400	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links