Variant report

Variant	rs9450765
Chromosome Location	chr6:88345048-88345049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11965607	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12663400	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13213729	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13220363	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35773999	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4330517	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4552702	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4707380	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6911782	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7748693	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7756133	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7768566	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7772351	0.82[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs910267	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9444515	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9444529	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450725	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450727	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450730	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450731	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450756	0.82[CHB][hapmap]
rs9450757	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450759	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9450765	EIF1AY	trans	lymphoblastoid	seeQTL
rs9450765	UTY	trans	lymphoblastoid	seeQTL
rs9450765	AKIRIN2	cis	cerebellum	SCAN
rs9450765	C6orf162	cis	cerebellum	SCAN
rs9450765	SLC35A1	cis	lymphoblastoid	seeQTL
rs9450765	C6orf162	cis	parietal	SCAN
rs9450765	DDX3Y	trans	lymphoblastoid	seeQTL
rs9450765	RPS4Y1	trans	lymphoblastoid	seeQTL
rs9450765	SLC35A1	cis	parietal	SCAN
rs9450765	KDM5D	trans	lymphoblastoid	seeQTL
rs9450765	SLC35A1	cis	multi-tissue	Pritchard
rs9450765	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88300600-88391200	Weak transcription	Colonic Mucosa	Colon
2	chr6:88301000-88347200	Weak transcription	Small Intestine	intestine
3	chr6:88301200-88385000	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:88301400-88354400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:88301400-88354600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:88302000-88347400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:88302000-88354400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:88302000-88354600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:88308800-88369800	Weak transcription	Fetal Brain Male	brain
11	chr6:88312200-88371200	Weak transcription	NHEK	skin
12	chr6:88312400-88380600	Weak transcription	Brain Substantia Nigra	brain
13	chr6:88314000-88384800	Weak transcription	Hela-S3	cervix
14	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:88314600-88385000	Weak transcription	Esophagus	oesophagus
16	chr6:88316600-88381200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:88316600-88390000	Weak transcription	Pancreas	Pancrea
18	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:88321200-88348400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:88321600-88350000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:88322000-88346200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr6:88322000-88352800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:88322800-88382000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:88323000-88346200	Weak transcription	Fetal Kidney	kidney
25	chr6:88323000-88366400	Weak transcription	A549	lung
26	chr6:88324000-88347400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:88324000-88369800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:88324000-88385000	Weak transcription	Gastric	stomach
29	chr6:88324200-88346000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:88324200-88346200	Weak transcription	Fetal Brain Female	brain
31	chr6:88324200-88350600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:88324200-88366600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:88324200-88369000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:88324200-88370200	Weak transcription	Psoas Muscle	Psoas
35	chr6:88324200-88378200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:88324200-88380400	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr6:88325400-88346200	Weak transcription	Left Ventricle	heart
38	chr6:88325400-88369200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:88327200-88362000	Weak transcription	Fetal Heart	heart
40	chr6:88327400-88346000	Weak transcription	Brain Anterior Caudate	brain
41	chr6:88328400-88357000	Weak transcription	HUVEC	blood vessel
42	chr6:88329800-88383200	Weak transcription	Lung	lung
43	chr6:88332200-88350200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr6:88332400-88346200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:88333400-88354600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr6:88333400-88384800	Weak transcription	Brain Angular Gyrus	brain
47	chr6:88333600-88346000	Weak transcription	Thymus	Thymus
48	chr6:88333600-88346400	Weak transcription	Aorta	Aorta
49	chr6:88333800-88346000	Weak transcription	HSMM	muscle
50	chr6:88334000-88346000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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