Variant report

Variant	rs1545496
Chromosome Location	chr12:45003574-45003575
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10785513	1.00[ASW][hapmap];0.92[CEU][hapmap];0.88[GIH][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11182552	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11182562	0.89[CEU][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12314678	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1470803	0.84[CHD][hapmap];0.86[GIH][hapmap]
rs17094865	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17094882	0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs2060839	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2060841	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2060842	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2060895	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2060896	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2060897	0.89[ASN][1000 genomes]
rs2060898	0.87[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2060899	0.82[CHD][hapmap];0.86[GIH][hapmap]
rs4641544	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768562	0.86[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6582508	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6582509	1.00[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7134952	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7304431	0.87[CHD][hapmap];0.91[GIH][hapmap]
rs7958608	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7966743	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7966744	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][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	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
4	esv3335202	chr12:45003513-45003972	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	n/a

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44986600-45006600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:44986800-45015800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:44990400-45004800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:44992200-45006400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:44993000-45006800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:44994400-45004200	Weak transcription	Brain Germinal Matrix	brain
7	chr12:44998000-45005600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:44998200-45024400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:44998600-45005000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr12:44998800-45004800	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr12:44998800-45018200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:44999600-45005000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:44999800-45003600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr12:45001600-45005200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:45001600-45009800	Weak transcription	Brain Angular Gyrus	brain
16	chr12:45001800-45005400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:45002600-45009600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr12:45003000-45004800	Strong transcription	Fetal Brain Female	brain
19	chr12:45003000-45005000	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:45003200-45014200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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