Variant report

Variant	rs4382065
Chromosome Location	chr4:78064766-78064767
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10010290	0.92[CEU][hapmap]
rs10025838	0.80[CEU][hapmap];0.85[GIH][hapmap]
rs1006042	0.92[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs11097704	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724432	0.86[JPT][hapmap]
rs11731592	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12504752	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12509168	0.80[CEU][hapmap]
rs12640093	0.80[CEU][hapmap];0.85[GIH][hapmap]
rs28464714	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28503908	0.86[JPT][hapmap]
rs4241604	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4280759	0.80[CEU][hapmap]
rs4302483	0.86[JPT][hapmap]
rs4365751	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4518274	0.84[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4544732	0.86[JPT][hapmap]
rs4547817	0.80[CEU][hapmap]
rs4558892	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4582179	0.92[CEU][hapmap]
rs4859473	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859751	0.86[JPT][hapmap]
rs4859756	0.83[GIH][hapmap]
rs6532867	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6532868	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6532870	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6532871	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6845942	0.83[EUR][1000 genomes]
rs6849124	0.86[JPT][hapmap]
rs6849534	0.86[JPT][hapmap]

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	nsv879500	chr4:78045960-78115334	Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4382065	BMP3	cis	parietal	SCAN
rs4382065	CCNG2	cis	cerebellum	SCAN
rs4382065	GDEP	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78059000-78067200	Weak transcription	Small Intestine	intestine
2	chr4:78059200-78067200	Weak transcription	Fetal Lung	lung
3	chr4:78062400-78065200	Enhancers	Fetal Intestine Large	intestine
4	chr4:78064000-78067600	Weak transcription	HSMMtube	muscle
5	chr4:78064200-78064800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:78064200-78065800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr4:78064200-78066200	Weak transcription	Brain Anterior Caudate	brain
8	chr4:78064200-78067000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:78064400-78064800	Enhancers	Duodenum Mucosa	Duodenum
10	chr4:78064400-78065800	Weak transcription	Fetal Intestine Small	intestine
11	chr4:78064600-78066400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr4:78064600-78066400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:78064600-78066600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:78064600-78067000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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