Variant report

Variant	rs3799095
Chromosome Location	chr6:70082863-70082864
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1283473	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1290329	0.81[ASW][hapmap];0.86[LWK][hapmap]
rs1328735	0.87[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1885331	0.83[LWK][hapmap];0.94[YRI][hapmap]
rs1928061	0.91[LWK][hapmap];0.88[YRI][hapmap]
rs2149457	0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs314197	0.87[YRI][hapmap]
rs6932340	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6939422	0.82[YRI][hapmap]
rs7745125	0.87[ASW][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.83[YRI][hapmap];0.86[ASN][1000 genomes]
rs7749882	0.80[ASW][hapmap];0.83[LWK][hapmap]
rs913543	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9454732	0.81[ASW][hapmap];0.83[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv432919	chr6:69873179-70221322	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv463149	chr6:70007450-70097588	Weak transcription Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv603635	chr6:70007450-70097588	Weak transcription Enhancers Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3799095	KHDC1	cis	parietal	SCAN
rs3799095	TSR1	trans	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70054600-70098600	Weak transcription	Brain Anterior Caudate	brain
2	chr6:70054600-70100600	Weak transcription	Brain Angular Gyrus	brain
3	chr6:70059200-70083200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:70081000-70083200	Weak transcription	Brain Germinal Matrix	brain
5	chr6:70081000-70086800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:70081000-70108000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:70081200-70084200	Weak transcription	Fetal Lung	lung
8	chr6:70081200-70094200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:70081200-70095200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:70082200-70098600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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