Variant report

Variant	rs13272793
Chromosome Location	chr8:10002027-10002028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10089339	1.00[CHB][hapmap]
rs10097184	1.00[CHB][hapmap]
rs10111917	1.00[CHB][hapmap]
rs10903321	1.00[CHB][hapmap]
rs11249970	0.94[YRI][hapmap]
rs11774220	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11776035	1.00[CHB][hapmap]
rs11776973	1.00[CHB][hapmap]
rs11780122	1.00[CHB][hapmap]
rs11783705	1.00[CHB][hapmap]
rs11785434	0.89[YRI][hapmap]
rs12156387	1.00[CHB][hapmap]
rs12678938	1.00[CHD][hapmap]
rs12679328	0.94[YRI][hapmap]
rs13250499	0.89[YRI][hapmap]
rs13252589	0.96[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13259465	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13261836	0.94[YRI][hapmap]
rs13263482	1.00[CHB][hapmap]
rs13279701	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1484641	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151658	1.00[CHB][hapmap]
rs17151667	1.00[CHB][hapmap]
rs17151675	1.00[CHB][hapmap]
rs17151684	1.00[CHB][hapmap]
rs17151699	1.00[CHB][hapmap]
rs17151713	1.00[CHB][hapmap]
rs17151728	1.00[CHB][hapmap]
rs17151741	1.00[CHB][hapmap]
rs17151745	1.00[CHB][hapmap]
rs17151748	1.00[CHB][hapmap]
rs17151763	1.00[CHB][hapmap]
rs17689007	0.81[CEU][hapmap]
rs17689037	0.81[CEU][hapmap]
rs17689289	0.81[CEU][hapmap]
rs17690549	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17693945	1.00[CHB][hapmap]
rs17694485	1.00[CHB][hapmap]
rs17707665	1.00[CHB][hapmap]
rs17707988	1.00[CHB][hapmap]
rs17708090	1.00[CHB][hapmap]
rs17708114	1.00[CHB][hapmap]
rs17746227	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17746245	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17747335	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17750324	1.00[CHB][hapmap]
rs17751178	1.00[CHB][hapmap]
rs2409632	0.94[YRI][hapmap]
rs34748716	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34990153	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35437983	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3885723	0.85[CEU][hapmap];0.83[MEX][hapmap]
rs4240640	1.00[CHB][hapmap]
rs4840462	0.94[YRI][hapmap]
rs4840467	1.00[CHB][hapmap]
rs4841294	1.00[CHB][hapmap]
rs4841295	1.00[CHB][hapmap]
rs4841296	1.00[CHB][hapmap]
rs4841312	1.00[CHB][hapmap]
rs60278284	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6985941	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6994060	1.00[CHB][hapmap]
rs6997224	1.00[CHB][hapmap]
rs6997865	0.89[YRI][hapmap]
rs7012221	0.89[YRI][hapmap]
rs7014570	1.00[CHB][hapmap]
rs7822745	1.00[CHB][hapmap]
rs7832431	0.94[YRI][hapmap]
rs7835507	1.00[CHB][hapmap]
rs7835960	1.00[CHB][hapmap]
rs7840347	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916493	chr8:9806580-10029482	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv610263	chr8:9941021-10090149	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1034343	chr8:9948342-10014155	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv831230	chr8:9953343-10139350	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1027280	chr8:9958259-10058984	Enhancers Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1021921	chr8:9958259-10212555	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv1850829	chr8:9958321-10045451	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv890344	chr8:9995515-10060638	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv831231	chr8:10001214-10189094	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13272793	MCPH1	cis	cerebellum	SCAN
rs13272793	PRSS55	cis	cerebellum	SCAN
rs13272793	FLJ10661	cis	cerebellum	SCAN
rs13272793	CLDN23	cis	multi-tissue	Pritchard
rs13272793	MSRA	cis	lymphoblastoid	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9986200-10002200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:9988800-10002200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr8:9991200-10004600	Weak transcription	Esophagus	oesophagus
4	chr8:9992200-10004800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr8:9992200-10004800	Weak transcription	Right Ventricle	heart
6	chr8:9996400-10020200	Weak transcription	Pancreas	Pancrea
7	chr8:9996600-10004600	Weak transcription	Gastric	stomach
8	chr8:9996600-10004800	Weak transcription	Left Ventricle	heart
9	chr8:9996600-10005000	Weak transcription	Right Atrium	heart
10	chr8:9996600-10036200	Weak transcription	Primary T cells from cord blood	blood
11	chr8:9996800-10009600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr8:9997000-10010200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr8:9997200-10002600	Weak transcription	Liver	Liver
14	chr8:10000000-10003000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr8:10000400-10003200	Flanking Active TSS	Brain Germinal Matrix	brain
16	chr8:10000600-10002600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr8:10000600-10002800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr8:10001000-10002200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr8:10001000-10002400	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr8:10001200-10002400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr8:10001200-10003800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr8:10001400-10002200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr8:10001400-10002400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr8:10001400-10002400	Enhancers	Brain Substantia Nigra	brain
25	chr8:10001400-10002800	Enhancers	H9 Cell Line	embryonic stem cell
26	chr8:10001400-10002800	Enhancers	Brain Angular Gyrus	brain
27	chr8:10001400-10004000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr8:10001400-10004800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr8:10001600-10002400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr8:10001600-10002600	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr8:10001600-10003000	Enhancers	Brain Hippocampus Middle	brain
32	chr8:10001600-10005000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr8:10001800-10002400	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr8:10001800-10002800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr8:10001800-10002800	Enhancers	Brain Anterior Caudate	brain
36	chr8:10001800-10003000	Enhancers	Brain Cingulate Gyrus	brain
37	chr8:10001800-10005800	Enhancers	Fetal Brain Male	brain
38	chr8:10002000-10002800	Enhancers	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links