Variant report

Variant	rs3734206
Chromosome Location	chr6:45922849-45922850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1001938	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11757345	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1204333	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1204334	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1204335	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12192179	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12198337	0.88[ASN][1000 genomes]
rs12211807	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1308732	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1890368	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1890369	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs1999908	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2396580	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777574	0.82[AFR][1000 genomes]
rs3777576	0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs3777577	0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs3777582	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3777583	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[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]
rs3777587	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777589	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777590	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777592	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822887	0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs4236087	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4236088	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4236089	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4429946	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4563714	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711834	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711835	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711836	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711837	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4714892	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4714893	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4714894	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4714895	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6909306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922752	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73460651	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3734206	GPR111	cis	parietal	SCAN
rs3734206	RSPH9	cis	parietal	SCAN
rs3734206	CDC5L	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45911000-45923600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr6:45912600-45923000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
3	chr6:45912800-45928400	Weak transcription	Spleen	Spleen
4	chr6:45917200-45924800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr6:45918800-45938400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:45919200-45923000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
7	chr6:45919200-45923200	Genic enhancers	Rectal Mucosa Donor 31	rectum
8	chr6:45919400-45923200	Strong transcription	Fetal Intestine Large	intestine
9	chr6:45919600-45923800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:45919600-45928000	Weak transcription	Adipose Nuclei	Adipose
11	chr6:45920000-45927200	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:45920000-45927200	Weak transcription	Placenta	Placenta
13	chr6:45920000-45928200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:45920000-45934800	Weak transcription	Colonic Mucosa	Colon
15	chr6:45920200-45926600	Weak transcription	Fetal Lung	lung
16	chr6:45920800-45924400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:45921200-45928200	Weak transcription	Lung	lung
18	chr6:45921400-45923200	Weak transcription	Fetal Intestine Small	intestine
19	chr6:45921400-45926800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:45922200-45923000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr6:45922200-45923200	Genic enhancers	Left Ventricle	heart
22	chr6:45922200-45923400	Enhancers	Fetal Heart	heart
23	chr6:45922400-45923200	Enhancers	Fetal Kidney	kidney
24	chr6:45922400-45923600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr6:45922400-45924800	Genic enhancers	Right Ventricle	heart
26	chr6:45922400-45925800	Enhancers	Psoas Muscle	Psoas
27	chr6:45922600-45923000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:45922600-45923200	Enhancers	Right Atrium	heart
29	chr6:45922800-45923200	Enhancers	Pancreas	Pancrea
30	chr6:45922800-45923800	Weak transcription	Duodenum Mucosa	Duodenum

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