Variant report

Variant	rs1075665
Chromosome Location	chr6:88366602-88366603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88365678..88369337-chr6:88379834..88383154,3	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1052623	0.94[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11962148	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs12524205	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12530371	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs13214442	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs16879893	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2246051	0.85[CHB][hapmap]
rs2246057	0.85[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap]
rs2268996	0.85[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap]
rs2295088	0.90[CHB][hapmap]
rs2300898	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2300899	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2300900	0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs2300904	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs2300908	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs3778671	0.85[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap]
rs3818057	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4354121	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs4707378	0.80[EUR][1000 genomes]
rs4707385	0.94[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4707386	0.84[ASN][1000 genomes]
rs58305152	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6454634	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6914244	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6927171	0.84[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs6928057	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7649	0.95[CHB][hapmap]
rs7761943	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs9294384	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9294385	0.81[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.86[ASN][1000 genomes]
rs9444509	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs9444514	0.93[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap]
rs9444521	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9444531	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9444534	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444536	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450697	0.84[CHB][hapmap]
rs9450698	0.85[CHB][hapmap]
rs9450699	0.95[CHB][hapmap]
rs9450700	0.95[CHB][hapmap]
rs9450708	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs9450709	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs9450716	0.85[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap]
rs9450717	0.85[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap]
rs9450740	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap]
rs9450749	0.93[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9450750	0.93[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9450751	0.81[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs9450756	0.93[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9450760	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450763	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450773	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450775	0.82[EUR][1000 genomes]
rs9474	0.94[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1075665	SLC35A1	cis	lymphoblastoid	seeQTL
rs1075665	C6orf162	cis	cerebellum	SCAN
rs1075665	AKIRIN2	cis	cerebellum	SCAN
rs1075665	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs1075665	SLC35A1	cis	multi-tissue	Pritchard
rs1075665	C6orf162	cis	parietal	SCAN
rs1075665	SLC35A1	cis	parietal	SCAN

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	chr6:88301200-88385000	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:88308800-88369800	Weak transcription	Fetal Brain Male	brain
5	chr6:88312200-88371200	Weak transcription	NHEK	skin
6	chr6:88312400-88380600	Weak transcription	Brain Substantia Nigra	brain
7	chr6:88314000-88384800	Weak transcription	Hela-S3	cervix
8	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:88314600-88385000	Weak transcription	Esophagus	oesophagus
10	chr6:88316600-88381200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:88316600-88390000	Weak transcription	Pancreas	Pancrea
12	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:88322800-88382000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:88324000-88369800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:88324000-88385000	Weak transcription	Gastric	stomach
16	chr6:88324200-88369000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:88324200-88370200	Weak transcription	Psoas Muscle	Psoas
18	chr6:88324200-88378200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:88324200-88380400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr6:88325400-88369200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:88329800-88383200	Weak transcription	Lung	lung
22	chr6:88333400-88384800	Weak transcription	Brain Angular Gyrus	brain
23	chr6:88338800-88369600	Weak transcription	HSMMtube	muscle
24	chr6:88339200-88396800	Weak transcription	Right Ventricle	heart
25	chr6:88340000-88370000	Weak transcription	Spleen	Spleen
26	chr6:88340600-88368400	Weak transcription	NHDF-Ad	bronchial
27	chr6:88344400-88384800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:88346400-88369600	Weak transcription	NH-A	brain
29	chr6:88346600-88373800	Weak transcription	Fetal Kidney	kidney
30	chr6:88346600-88376400	Weak transcription	Brain Hippocampus Middle	brain
31	chr6:88347800-88369200	Weak transcription	HSMM	muscle
32	chr6:88347800-88378000	Weak transcription	Fetal Brain Female	brain
33	chr6:88348000-88367000	Weak transcription	Osteobl	bone
34	chr6:88348000-88369200	Weak transcription	Aorta	Aorta
35	chr6:88348000-88385000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:88348600-88377600	Weak transcription	Brain Anterior Caudate	brain
37	chr6:88349000-88369600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr6:88349200-88373200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:88349200-88381400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:88349400-88366800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr6:88349400-88366800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr6:88349400-88377800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr6:88349400-88385000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr6:88349400-88397400	Weak transcription	Ovary	ovary
45	chr6:88349800-88369200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:88350800-88369200	Weak transcription	Fetal Stomach	stomach
47	chr6:88351800-88368200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr6:88355200-88379400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr6:88356600-88380400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:88357000-88369200	Weak transcription	Adipose Nuclei	Adipose

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