Variant report

Variant	rs1328735
Chromosome Location	chr6:70097588-70097589
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1283473	0.82[EUR][1000 genomes]
rs1290329	0.81[ASW][hapmap];0.80[LWK][hapmap]
rs1885331	0.88[YRI][hapmap]
rs1928061	0.86[ASW][hapmap];0.91[LWK][hapmap];0.94[YRI][hapmap]
rs1952435	0.81[ASW][hapmap];0.80[LWK][hapmap]
rs2149457	0.87[ASW][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs3799095	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]
rs6932340	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7745125	0.87[ASW][hapmap];0.91[CHD][hapmap];0.80[LWK][hapmap];0.81[ASN][1000 genomes]
rs7749882	0.80[ASW][hapmap]
rs913543	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9454732	0.81[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv463149	chr6:70007450-70097588	Weak transcription Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	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
rs1328735	KHDC1	cis	parietal	SCAN
rs1328735	TSR1	trans	parietal	SCAN

Chromatin state (count:13 , 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	chr6:70081000-70108000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:70082200-70098600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:70088200-70099600	Weak transcription	Small Intestine	intestine
6	chr6:70092600-70100200	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:70094600-70098400	Weak transcription	Fetal Lung	lung
8	chr6:70095800-70098400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr6:70095800-70102200	Weak transcription	Brain Germinal Matrix	brain
10	chr6:70096000-70098400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:70096000-70101600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:70097200-70099800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr6:70097200-70109000	Weak transcription	Fetal Brain Male	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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