Variant report

Variant	rs1271629
Chromosome Location	chr10:50956158-50956159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:50950802..50953710-chr10:50955807..50957980,3	K562	blood:
2	chr10:50953927..50957241-chr10:50965194..50969750,5	K562	blood:
3	chr10:50954773..50957241-chr10:50965884..50969750,3	K562	blood:

Variant related genes	Relation type
ENSG00000197444	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11101218	0.91[EUR][1000 genomes]
rs1125165	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1258168	0.96[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1258169	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1258170	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1258176	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258178	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258179	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258181	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258182	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258184	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258201	0.89[JPT][hapmap]
rs1258204	0.89[JPT][hapmap]
rs1258241	0.81[CEU][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap]
rs1258243	0.85[EUR][1000 genomes]
rs1258245	0.92[EUR][1000 genomes]
rs1258246	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1258247	0.85[EUR][1000 genomes]
rs1258249	0.85[EUR][1000 genomes]
rs1258250	0.85[EUR][1000 genomes]
rs1258251	0.84[EUR][1000 genomes]
rs1258252	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1258253	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1258255	0.88[EUR][1000 genomes]
rs1258256	0.92[CEU][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1258258	0.96[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1258260	0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1258323	0.81[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs1258326	0.81[CEU][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs1258329	0.84[EUR][1000 genomes]
rs1258330	0.85[EUR][1000 genomes]
rs1268722	0.96[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1268723	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1270562	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13736	0.89[CHB][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.87[EUR][1000 genomes]
rs1625258	0.85[EUR][1000 genomes]
rs1659305	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2889729	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4372365	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6537552	0.84[GIH][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6816	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]
rs745836	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs745837	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs745838	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
rs1271629	DRGX	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50940600-50966000	Strong transcription	Liver	Liver
2	chr10:50941200-50965400	Weak transcription	Brain Germinal Matrix	brain
3	chr10:50943000-50956400	Strong transcription	Brain Anterior Caudate	brain
4	chr10:50943200-50969400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr10:50943400-50956200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:50944000-50969400	Weak transcription	Brain Substantia Nigra	brain
7	chr10:50947800-50960400	Strong transcription	Brain Angular Gyrus	brain
8	chr10:50948000-50956600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr10:50948800-50956600	Strong transcription	Brain Inferior Temporal Lobe	brain
10	chr10:50949600-50956200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr10:50951600-50969200	Weak transcription	Fetal Intestine Large	intestine
12	chr10:50952400-50956600	Strong transcription	Brain Cingulate Gyrus	brain
13	chr10:50952600-50968800	Weak transcription	Pancreas	Pancrea
14	chr10:50953400-50969400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr10:50954400-50962400	Weak transcription	Brain Hippocampus Middle	brain
16	chr10:50954600-50958200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr10:50954800-50959400	Weak transcription	Right Atrium	heart
18	chr10:50955000-50958600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr10:50955000-50967800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr10:50955000-50969000	Weak transcription	Ovary	ovary
21	chr10:50955000-50969400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr10:50955200-50964200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr10:50955400-50958800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr10:50955400-50959600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr10:50955400-50960200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr10:50955600-50957400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr10:50955600-50957600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr10:50955600-50957600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:50955600-50957600	Weak transcription	Fetal Intestine Small	intestine
30	chr10:50955600-50958000	Weak transcription	Spleen	Spleen
31	chr10:50955600-50958400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr10:50955600-50959400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr10:50956000-50956200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links