Variant report

Variant	rs4768564
Chromosome Location	chr12:45014924-45014925
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1037433	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1037434	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506256	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10748400	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10785515	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880655	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs10880657	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880658	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880659	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880660	0.94[ASN][1000 genomes]
rs10880666	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs10880673	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs11182552	0.90[YRI][hapmap]
rs11182556	0.80[YRI][hapmap]
rs11182559	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11182560	0.81[YRI][hapmap]
rs11182562	0.91[YRI][hapmap]
rs11182596	0.94[ASN][1000 genomes]
rs11182599	0.88[ASN][1000 genomes]
rs11182636	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs12815257	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1563043	1.00[CEU][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1850406	0.90[CHD][hapmap];0.91[GIH][hapmap]
rs1869162	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1966855	0.95[EUR][1000 genomes]
rs2060839	0.90[YRI][hapmap]
rs2060840	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2060841	0.90[YRI][hapmap]
rs2060842	0.90[YRI][hapmap]
rs2060895	0.84[ASW][hapmap];0.90[YRI][hapmap]
rs2060896	0.84[ASW][hapmap];0.90[YRI][hapmap]
rs2084843	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305448	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4544065	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4768066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768563	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs583575	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[ASN][1000 genomes]
rs605722	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs615760	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[ASN][1000 genomes]
rs628408	0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[YRI][hapmap];0.88[ASN][1000 genomes]
rs632481	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs636843	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[ASN][1000 genomes]
rs6582509	0.84[ASW][hapmap];0.90[YRI][hapmap]
rs678663	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs688669	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7295999	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7299365	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[ASN][1000 genomes]
rs7300005	0.84[YRI][hapmap]
rs7301539	0.94[ASN][1000 genomes]
rs7308509	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap]
rs7310844	0.94[ASN][1000 genomes]
rs7314643	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs765769	0.95[EUR][1000 genomes]
rs7958389	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7958608	0.84[ASW][hapmap];0.90[YRI][hapmap]
rs7968076	0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7970849	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs838973	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs966383	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs978540	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049818	chr12:44486312-45133783	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3378050	chr12:44963059-45264289	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv430506	chr12:45003342-45072343	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4768564	TMEM117	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44986800-45015800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:44998200-45024400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:44998800-45018200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:45004800-45020800	Weak transcription	Fetal Brain Female	brain
5	chr12:45004800-45034800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr12:45004800-45043200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:45005000-45023200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:45005000-45031200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:45005000-45044200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr12:45011800-45015800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:45013400-45019000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:45013800-45020200	Weak transcription	Fetal Brain Male	brain
13	chr12:45014200-45015000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:45014400-45015200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:45014800-45015800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links