Variant report

Variant	rs41396347
Chromosome Location	chr2:142251661-142251662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10496881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887304	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11898305	0.82[JPT][hapmap]
rs13408702	0.85[YRI][hapmap]
rs13415966	0.85[YRI][hapmap]
rs1483144	0.85[JPT][hapmap]
rs16846183	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846272	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846416	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs16846509	1.00[JPT][hapmap]
rs16846539	1.00[JPT][hapmap]
rs16855055	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17738291	0.82[JPT][hapmap]
rs1905291	0.85[JPT][hapmap]
rs4073067	0.85[YRI][hapmap]
rs4271711	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4491668	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4547471	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4560051	0.85[JPT][hapmap]
rs4575660	0.85[JPT][hapmap]
rs4954914	0.85[JPT][hapmap]
rs62167901	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs62167934	0.85[ASN][1000 genomes]
rs62167935	0.85[ASN][1000 genomes]
rs6429898	0.84[JPT][hapmap]
rs6708984	0.82[JPT][hapmap]
rs6717169	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs6749551	0.85[JPT][hapmap]
rs72849629	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72849660	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72849666	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72851323	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72851325	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72851386	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72852436	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72852464	0.95[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7557886	0.82[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7576810	0.85[ASN][1000 genomes]
rs9287319	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

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	nsv817518	chr2:141714174-142287302	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv583203	chr2:142055133-142378975	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv875234	chr2:142156180-142254119	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	nsv875240	chr2:142199421-142347455	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
5	nsv875243	chr2:142219033-142259592	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	nsv459607	chr2:142226768-142263400	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	nsv583207	chr2:142226768-142263400	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	nsv459618	chr2:142246988-142263746	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	nsv583209	chr2:142246988-142263746	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142239400-142256400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:142247800-142266200	Weak transcription	Brain Anterior Caudate	brain
3	chr2:142249600-142254800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:142249600-142257600	Weak transcription	Brain Substantia Nigra	brain
5	chr2:142250000-142255000	Weak transcription	NH-A	brain
6	chr2:142250200-142254800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:142251000-142251800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:142251000-142251800	Enhancers	Esophagus	oesophagus
9	chr2:142251600-142251800	Enhancers	Brain Inferior Temporal Lobe	brain

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