Variant report

Variant	rs3798997
Chromosome Location	chr6:69708219-69708220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10455681	1.00[LWK][hapmap];1.00[MKK][hapmap]
rs12665384	1.00[ASW][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12665411	0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1336654	1.00[CEU][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1415032	0.80[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1572940	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1953614	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2022212	1.00[LWK][hapmap]
rs3757049	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3798971	0.86[JPT][hapmap]
rs3798982	0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3798983	0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3798990	0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3798995	0.82[ASW][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3799019	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3823070	1.00[LWK][hapmap];1.00[MKK][hapmap]
rs688606	0.84[MKK][hapmap]
rs72906776	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs779484	0.84[MKK][hapmap]
rs9360369	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs960991	0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9718113	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

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:21 , 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	chr6:69696400-69715400	Weak transcription	Aorta	Aorta
5	chr6:69700800-69710200	Weak transcription	Brain Anterior Caudate	brain
6	chr6:69701000-69723000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:69701000-69737600	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:69701200-69721200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:69701200-69724400	Weak transcription	Brain Germinal Matrix	brain
10	chr6:69702400-69728600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:69702400-69737600	Weak transcription	Brain Angular Gyrus	brain
12	chr6:69702600-69723800	Weak transcription	Brain Substantia Nigra	brain
13	chr6:69703800-69719400	Weak transcription	Fetal Brain Female	brain
14	chr6:69704800-69708400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:69704800-69713000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:69704800-69721600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:69705400-69711600	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:69706400-69720800	Weak transcription	Fetal Lung	lung
19	chr6:69706600-69721600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:69708200-69708400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr6:69708200-69708600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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