Variant report

Variant	rs9314526
Chromosome Location	chr8:4196759-4196760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10086105	0.88[JPT][hapmap]
rs10091031	0.87[ASW][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10091134	0.95[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10094349	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10103498	1.00[JPT][hapmap]
rs10103842	0.88[ASN][1000 genomes]
rs10103969	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10105113	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10105349	0.80[JPT][hapmap]
rs10107472	0.81[ASW][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10108270	0.89[ASW][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs10108725	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10108980	0.82[ASN][1000 genomes]
rs10429391	1.00[ASW][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[YRI][hapmap]
rs10866968	0.94[JPT][hapmap]
rs12679965	0.81[ASN][1000 genomes]
rs13268424	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1504754	0.81[CHB][hapmap]
rs1546356	0.84[ASN][1000 genomes]
rs1866271	0.87[ASW][hapmap];0.92[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2062879	1.00[YRI][hapmap]
rs4875336	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs4875337	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6558864	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6558865	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6558868	1.00[ASW][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap]
rs7000582	0.91[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7009827	0.80[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap]
rs7010684	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7015864	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7832549	1.00[ASW][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949269	chr8:3556145-4246903	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv530863	chr8:3710810-4381378	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv530531	chr8:3942575-4605088	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1034771	chr8:3969767-4255716	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv889939	chr8:4033186-4718648	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1032488	chr8:4072826-4328057	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1019677	chr8:4095786-4328057	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1015485	chr8:4127704-4272847	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv34054	chr8:4165205-4450873	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9314526	MCPH1	cis	cerebellum	SCAN
rs9314526	XKR5	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:4190000-4199600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr8:4194200-4202600	Weak transcription	Pancreas	Pancrea
3	chr8:4194400-4197000	Enhancers	Fetal Intestine Large	intestine
4	chr8:4194600-4197400	Enhancers	Liver	Liver
5	chr8:4194800-4202600	Weak transcription	Gastric	stomach
6	chr8:4195200-4199200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr8:4195400-4196800	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr8:4196200-4197000	Enhancers	Fetal Intestine Small	intestine
9	chr8:4196400-4196800	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr8:4196400-4197600	Enhancers	Stomach Mucosa	stomach
11	chr8:4196400-4198800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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