Variant report

Variant	rs4599051
Chromosome Location	chr2:142253903-142253904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10169644	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10169745	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10173806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10184273	0.84[CEU][hapmap]
rs10204321	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10204413	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10204518	0.80[CEU][hapmap]
rs10204727	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10496882	0.81[TSI][hapmap]
rs10928105	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10928107	0.81[YRI][hapmap]
rs11681928	0.81[MEX][hapmap]
rs11895715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12053264	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12053266	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12053452	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12053570	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12053574	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12151429	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12151669	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12467062	0.95[JPT][hapmap];0.81[MEX][hapmap]
rs12472514	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12478973	0.87[JPT][hapmap];0.85[MEX][hapmap]
rs12611851	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12621499	0.95[JPT][hapmap];0.81[MEX][hapmap]
rs12622205	0.83[ASN][1000 genomes]
rs13007713	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs13013202	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13023434	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13031144	0.80[MEX][hapmap]
rs13391905	0.81[CEU][hapmap]
rs13411666	0.85[ASN][1000 genomes]
rs13418036	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13418422	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1483141	0.95[JPT][hapmap]
rs16846151	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16846521	0.90[MEX][hapmap]
rs2200192	0.82[JPT][hapmap]
rs2381190	0.90[MEX][hapmap]
rs34333390	0.80[EUR][1000 genomes]
rs4245858	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4264514	0.82[CEU][hapmap]
rs4271710	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4296374	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4327189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4338922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4340449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4375803	0.81[YRI][hapmap]
rs4384715	0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.86[ASN][1000 genomes]
rs4402694	0.81[YRI][hapmap]
rs4430882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4476293	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4507040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4544370	0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4574055	0.86[MEX][hapmap]
rs4583399	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4635467	0.95[YRI][hapmap]
rs4644970	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4954910	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4954912	0.81[EUR][1000 genomes]
rs60118950	0.82[ASN][1000 genomes]
rs62166338	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62167876	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429887	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6429889	0.82[ASN][1000 genomes]
rs6429890	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6429891	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6429892	0.93[ASN][1000 genomes]
rs6429894	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6723276	0.81[CEU][hapmap]
rs6725282	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6729073	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6729618	0.96[ASN][1000 genomes]
rs6729691	0.95[ASN][1000 genomes]
rs6738081	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6759197	0.80[EUR][1000 genomes]
rs68142404	0.86[ASN][1000 genomes]
rs72849086	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7340298	0.96[ASN][1000 genomes]
rs7340300	0.89[ASN][1000 genomes]
rs7340384	0.95[ASN][1000 genomes]
rs7568338	0.92[YRI][hapmap]
rs7569047	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7583765	0.86[ASN][1000 genomes]
rs7593962	0.95[JPT][hapmap]
rs9287318	0.81[CEU][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4599051	TTLL6	trans	parietal	SCAN

Chromatin state (count:7 , 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	chr2:142252800-142255000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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