Variant report

Variant	rs6816
Chromosome Location	chr10:50942763-50942764
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11101218	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1125165	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1258168	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1258169	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1258170	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1258176	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1258178	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1258179	0.81[CEU][hapmap];0.89[CHB][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1258181	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1258182	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1258184	0.81[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1258201	0.89[JPT][hapmap];0.80[MEX][hapmap]
rs1258204	0.89[JPT][hapmap];0.80[MEX][hapmap];0.82[MKK][hapmap]
rs1258228	0.80[EUR][1000 genomes]
rs1258241	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.87[YRI][hapmap]
rs1258243	0.85[EUR][1000 genomes]
rs1258245	0.94[EUR][1000 genomes]
rs1258246	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1258247	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1258249	0.85[EUR][1000 genomes]
rs1258250	0.85[EUR][1000 genomes]
rs1258251	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1258252	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1258253	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1258255	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258256	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258258	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258260	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1258323	0.92[CEU][hapmap];0.81[JPT][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1258326	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1258329	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1258330	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1268722	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1268723	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1270562	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1271629	0.88[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13736	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1625258	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1659305	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2889729	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4372365	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6537552	0.83[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs745836	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs745837	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs745838	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv895378	chr10:50801342-50955649	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1048905	chr10:50928727-51019190	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6816	DRGX	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50934800-50944000	Weak transcription	Brain Angular Gyrus	brain
2	chr10:50935200-50943000	Weak transcription	Brain Anterior Caudate	brain
3	chr10:50935200-50949600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:50935400-50943600	Weak transcription	Fetal Brain Female	brain
5	chr10:50939000-50944200	Weak transcription	Pancreas	Pancrea
6	chr10:50939400-50943600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr10:50940000-50942800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr10:50940200-50943200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr10:50940400-50949600	Weak transcription	Fetal Heart	heart
10	chr10:50940400-50953400	Weak transcription	Brain Hippocampus Middle	brain
11	chr10:50940600-50966000	Strong transcription	Liver	Liver
12	chr10:50941000-50942800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr10:50941000-50946400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr10:50941000-50951600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr10:50941200-50943000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr10:50941200-50943800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr10:50941200-50945000	Weak transcription	Spleen	Spleen
18	chr10:50941200-50965400	Weak transcription	Brain Germinal Matrix	brain
19	chr10:50941400-50942800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr10:50941400-50942800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr10:50941600-50943200	Weak transcription	Ovary	ovary
22	chr10:50941600-50943400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr10:50941600-50943400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr10:50941800-50943400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr10:50941800-50943400	Weak transcription	Brain Substantia Nigra	brain
26	chr10:50941800-50943600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr10:50942000-50943400	Enhancers	Fetal Intestine Large	intestine
28	chr10:50942000-50946400	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr10:50942000-50949600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr10:50942400-50943200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr10:50942600-50943000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr10:50942600-50943200	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links