Variant report

Variant	rs3799002
Chromosome Location	chr6:69715466-69715467
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1007921	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12194774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs12213405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs13191563	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs13191706	0.80[ASN][1000 genomes]
rs13192798	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13194716	0.80[ASN][1000 genomes]
rs13197569	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs13205016	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs13205140	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs13219339	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs1336634	1.00[JPT][hapmap]
rs1336635	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1336636	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1336651	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1336655	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1384246	1.00[JPT][hapmap]
rs1415029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415036	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1482323	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs1556756	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16900400	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1842743	1.00[JPT][hapmap]
rs1889877	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1889878	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2128290	1.00[JPT][hapmap]
rs2170508	1.00[JPT][hapmap]
rs2170509	1.00[JPT][hapmap]
rs2200088	1.00[JPT][hapmap]
rs2210867	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2225803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2343396	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2785576	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs2793459	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs34526480	0.80[ASN][1000 genomes]
rs35797298	0.81[ASN][1000 genomes]
rs3734465	1.00[JPT][hapmap]
rs3757045	0.80[ASN][1000 genomes]
rs3757046	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3757047	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3757051	1.00[JPT][hapmap]
rs3798996	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs3798999	0.89[YRI][hapmap];0.88[AFR][1000 genomes]
rs3799000	0.83[CEU][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs3799007	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3799016	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3799017	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3799021	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3799023	1.00[JPT][hapmap]
rs3799028	1.00[JPT][hapmap]
rs3799030	1.00[JPT][hapmap]
rs3799039	1.00[JPT][hapmap]
rs3823066	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3823067	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4554293	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs524359	1.00[JPT][hapmap]
rs526898	0.89[CEU][hapmap]
rs557184	1.00[JPT][hapmap]
rs570181	1.00[JPT][hapmap]
rs602406	1.00[JPT][hapmap]
rs634371	0.89[CEU][hapmap]
rs634695	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs635863	1.00[JPT][hapmap]
rs6455309	1.00[JPT][hapmap]
rs653895	1.00[JPT][hapmap]
rs6903686	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs6904267	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6908180	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs6930865	1.00[JPT][hapmap]
rs6934473	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs71555397	0.80[ASN][1000 genomes]
rs7739849	1.00[JPT][hapmap]
rs7741493	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7743332	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7756040	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7756358	1.00[JPT][hapmap]
rs7756637	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7760307	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7761270	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs7764479	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7767118	1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs779017	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs9342740	1.00[JPT][hapmap]
rs9346261	1.00[JPT][hapmap]
rs9360371	1.00[JPT][hapmap]
rs9360372	1.00[JPT][hapmap]
rs9446085	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9454670	0.85[AFR][1000 genomes]
rs9454674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454695	1.00[JPT][hapmap]
rs947221	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs964664	1.00[JPT][hapmap]
rs994381	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886137	chr6:69684850-70095690	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69685800-69758800	Weak transcription	Fetal Brain Male	brain
2	chr6:69688200-69721200	Weak transcription	Left Ventricle	heart
3	chr6:69692000-69716600	Weak transcription	Fetal Stomach	stomach
4	chr6:69701000-69723000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:69701000-69737600	Weak transcription	Brain Hippocampus Middle	brain
6	chr6:69701200-69721200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:69701200-69724400	Weak transcription	Brain Germinal Matrix	brain
8	chr6:69702400-69728600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:69702400-69737600	Weak transcription	Brain Angular Gyrus	brain
10	chr6:69702600-69723800	Weak transcription	Brain Substantia Nigra	brain
11	chr6:69703800-69719400	Weak transcription	Fetal Brain Female	brain
12	chr6:69704800-69721600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:69706400-69720800	Weak transcription	Fetal Lung	lung
14	chr6:69706600-69721600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:69711600-69717600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:69713000-69721400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:69714600-69715600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:69715200-69715600	Enhancers	NH-A	brain
19	chr6:69715400-69715600	Enhancers	Aorta	Aorta
20	chr6:69715400-69715800	Enhancers	Placenta	Placenta

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