Variant report

Variant	rs9444525
Chromosome Location	chr6:88324142-88324143
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	chr6:88323620..88325192-chr6:88338227..88341168,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1051131	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1051148	0.80[EUR][1000 genomes]
rs10755484	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13193380	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13194003	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2246113	0.86[EUR][1000 genomes]
rs2300906	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2307379	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2325064	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2754247	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2754248	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2754260	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2754262	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2787893	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2787921	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2787924	0.92[EUR][1000 genomes]
rs2814712	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3757368	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3934838	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4334949	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4464759	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4498321	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4587138	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4587143	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4706294	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4707373	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4707374	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4707376	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4707377	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4707379	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707382	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4707383	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6454631	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6454632	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6454636	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6454638	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6454640	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6454641	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6906769	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6908386	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6916732	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6918909	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6923230	0.81[ASN][1000 genomes]
rs6928160	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6930600	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6931069	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6940150	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7741825	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7742965	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7746465	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7750207	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7752494	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7755167	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7757636	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7757794	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7762864	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7772561	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7773906	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9444512	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444519	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9444522	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444524	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444526	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444530	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450723	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450726	0.82[ASN][1000 genomes]
rs9450732	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450733	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450738	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450739	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450744	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450752	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450755	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450762	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs985764	0.80[EUR][1000 genomes];0.81[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9444525	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs9444525	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs9444525	C6orf166	Cis_1M	lymphoblastoid	RTeQTL
rs9444525	SLC35A1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 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	chr6:88301000-88330200	Weak transcription	Right Ventricle	heart
3	chr6:88301000-88347200	Weak transcription	Small Intestine	intestine
4	chr6:88301200-88385000	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:88301400-88338400	Weak transcription	NHLF	lung
6	chr6:88301400-88354400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:88301400-88354600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:88302000-88347400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:88302000-88354400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:88302000-88354600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:88305200-88329000	Weak transcription	HSMMtube	muscle
13	chr6:88305800-88325200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:88308800-88369800	Weak transcription	Fetal Brain Male	brain
15	chr6:88311400-88334600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:88312200-88371200	Weak transcription	NHEK	skin
17	chr6:88312400-88380600	Weak transcription	Brain Substantia Nigra	brain
18	chr6:88313800-88338200	Weak transcription	NHDF-Ad	bronchial
19	chr6:88314000-88384800	Weak transcription	Hela-S3	cervix
20	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr6:88314600-88385000	Weak transcription	Esophagus	oesophagus
22	chr6:88315200-88327000	Weak transcription	Fetal Heart	heart
23	chr6:88315400-88327000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr6:88315400-88334600	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr6:88315800-88324400	Strong transcription	Placenta	Placenta
26	chr6:88315800-88324400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr6:88315800-88326800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:88315800-88327000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:88315800-88327200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:88316000-88324200	Strong transcription	Dnd41	blood
31	chr6:88316000-88325200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:88316200-88324400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:88316400-88330600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:88316600-88328200	Weak transcription	HUVEC	blood vessel
35	chr6:88316600-88381200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:88316600-88390000	Weak transcription	Pancreas	Pancrea
37	chr6:88316800-88324800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr6:88316800-88337800	Weak transcription	GM12878-XiMat	blood
39	chr6:88317200-88324400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:88317400-88325400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:88317600-88325000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr6:88317800-88325200	Strong transcription	Stomach Smooth Muscle	stomach
43	chr6:88318600-88324200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:88318800-88324800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:88319000-88333000	Weak transcription	HepG2	liver
46	chr6:88319400-88324200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:88319800-88324200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:88319800-88324200	Strong transcription	Fetal Brain Female	brain
49	chr6:88319800-88325400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:88320000-88324200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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