Variant report

Variant	rs3798993
Chromosome Location	chr6:69698592-69698593
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1006997	0.91[JPT][hapmap]
rs1336641	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1336645	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1336646	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1336647	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1336648	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1336649	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1336650	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs1415030	0.86[JPT][hapmap]
rs1556754	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1556755	0.85[ASN][1000 genomes]
rs1932774	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1953615	0.85[ASN][1000 genomes]
rs1999787	0.86[JPT][hapmap]
rs1999788	0.98[ASN][1000 genomes]
rs2860121	0.86[JPT][hapmap]
rs2880587	1.00[JPT][hapmap]
rs2880588	0.93[ASN][1000 genomes]
rs3798969	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs3798974	1.00[JPT][hapmap]
rs3798979	0.92[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[YRI][hapmap];0.90[ASN][1000 genomes]
rs3798983	0.82[JPT][hapmap]
rs3798988	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3798991	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798992	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3823064	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[YRI][hapmap];0.90[ASN][1000 genomes]
rs6899467	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7757025	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs9354812	0.86[JPT][hapmap]
rs9446079	0.93[ASN][1000 genomes]
rs9454661	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[YRI][hapmap];0.91[ASN][1000 genomes]
rs945528	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs945529	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv5338	chr6:69670701-69701360	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3798993	C6orf155	cis	parietal	SCAN
rs3798993	KRT4	trans	parietal	SCAN
rs3798993	C6orf57	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69685000-69700000	Weak transcription	Brain Angular Gyrus	brain
2	chr6:69685400-69700400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:69685800-69758800	Weak transcription	Fetal Brain Male	brain
4	chr6:69686000-69700000	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:69686000-69700400	Weak transcription	Brain Anterior Caudate	brain
6	chr6:69686000-69700600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:69686200-69703400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:69686600-69700200	Weak transcription	Brain Substantia Nigra	brain
9	chr6:69686800-69706200	Weak transcription	Fetal Lung	lung
10	chr6:69687800-69700400	Weak transcription	Brain Germinal Matrix	brain
11	chr6:69688200-69721200	Weak transcription	Left Ventricle	heart
12	chr6:69692000-69716600	Weak transcription	Fetal Stomach	stomach
13	chr6:69695200-69704400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:69695600-69700200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:69695800-69700200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:69696200-69703400	Weak transcription	Fetal Brain Female	brain
17	chr6:69696400-69715400	Weak transcription	Aorta	Aorta

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