Variant report

Variant	rs12502993
Chromosome Location	chr4:47276305-47276306
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10003607	0.88[CHB][hapmap]
rs10009164	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.94[EUR][1000 genomes]
rs10016815	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes]
rs10016894	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes]
rs10017723	0.83[CHB][hapmap]
rs10018597	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs10805153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11727759	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs11931599	0.97[EUR][1000 genomes]
rs1372497	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes]
rs1372498	0.88[CHB][hapmap]
rs1372499	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes]
rs1442091	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs1442108	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes]
rs1442109	0.84[CHB][hapmap]
rs1470208	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes]
rs1583952	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.89[EUR][1000 genomes]
rs16860067	0.95[EUR][1000 genomes]
rs16860071	0.94[EUR][1000 genomes]
rs16860083	0.89[CHB][hapmap]
rs16860087	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs28482891	0.93[EUR][1000 genomes]
rs28498348	0.95[EUR][1000 genomes]
rs28587597	0.93[EUR][1000 genomes]
rs28605268	0.92[ASN][1000 genomes]
rs3098797	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.97[EUR][1000 genomes]
rs3098799	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3098802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs3114084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs3114088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3114089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4403026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4426746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4481218	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes]
rs4586906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4695200	0.86[EUR][1000 genomes]
rs4695201	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[EUR][1000 genomes]
rs4695202	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs6447541	0.88[CHB][hapmap]
rs6834646	0.84[CHB][hapmap]
rs7666487	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.97[EUR][1000 genomes]
rs7671741	0.94[CHB][hapmap]
rs7695365	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap]

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	nsv1009766	chr4:47155845-47277391	Enhancers Flanking Active TSS Weak transcription Active TSS	lncRNA	n/a	inside rSNPs	diseases
2	nsv998919	chr4:47207023-47476876	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv879004	chr4:47234200-47322190	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47272400-47280600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr4:47273200-47280600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:47273600-47277200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr4:47273600-47277400	Weak transcription	Brain Anterior Caudate	brain
5	chr4:47273600-47280400	Weak transcription	Brain Angular Gyrus	brain
6	chr4:47273600-47280800	Weak transcription	Brain Germinal Matrix	brain
7	chr4:47274200-47277600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:47274400-47280000	Weak transcription	Fetal Brain Female	brain
9	chr4:47275200-47279600	Enhancers	Fetal Brain Male	brain
10	chr4:47275400-47280000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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