Variant report

Variant	rs9444519
Chromosome Location	chr6:88290398-88290399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88182686..88185163-chr6:88288656..88290504,2	K562	blood:
2	chr6:88285212..88293434-chr6:88297589..88302538,14	K562	blood:
3	chr6:88126441..88128032-chr6:88288832..88291183,2	MCF-7	breast:
4	chr6:88287850..88291294-chr6:88408676..88413224,5	MCF-7	breast:
5	chr6:88284821..88286391-chr6:88289308..88290910,2	K562	blood:
6	chr6:88285921..88288874-chr6:88289679..88293937,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135336	Chromatin interaction
ENSG00000135334	Chromatin interaction
ENSG00000164414	Chromatin interaction
ENSG00000146282	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1051131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1051148	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10755484	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13193380	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13194003	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13214153	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs2207144	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs2207146	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2246113	0.96[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs2268993	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs2268994	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs2273129	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2284908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2300906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2300909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2307379	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2325064	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2754245	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2754247	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2754248	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2754260	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2754262	0.96[CEU][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs2787893	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2787921	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2787924	0.89[EUR][1000 genomes]
rs2787927	0.96[CEU][hapmap];0.90[JPT][hapmap]
rs2814712	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3757368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3918467	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs3934838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4334949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4464759	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4498321	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4587138	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4587143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4706294	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4707373	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4707374	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4707376	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4707377	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4707379	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4707382	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4707383	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6454630	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs6454631	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6454632	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6454636	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6454638	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6454640	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6454641	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6905947	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs6906769	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6908386	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6914299	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs6916732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6918909	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6923230	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6928160	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6930600	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6931069	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6933587	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs6940150	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741825	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7742965	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7746465	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7750207	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7752494	0.82[EUR][1000 genomes]
rs7754350	0.86[ASN][1000 genomes]
rs7755167	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7756225	0.81[ASN][1000 genomes]
rs7757636	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7757794	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7761814	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs7762864	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7772561	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7773906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9294379	0.91[CHB][hapmap]
rs9294380	0.82[CEU][hapmap]
rs9294381	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs9444504	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs9444512	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444522	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9444524	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9444525	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9444526	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9444530	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450701	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs9450704	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs9450712	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9450723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450726	0.91[ASN][1000 genomes]
rs9450732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450733	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450738	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450739	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450744	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450752	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450755	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450762	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs985764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv538354	chr6:88273858-88311606	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9444519	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs9444519	C6orf166	Cis_1M	lymphoblastoid	RTeQTL
rs9444519	SLC35A1	cis	multi-tissue	Pritchard
rs9444519	C6orf162	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88217800-88295800	Weak transcription	Fetal Brain Male	brain
2	chr6:88227800-88298800	Weak transcription	Esophagus	oesophagus
3	chr6:88228400-88298400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:88251000-88291400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:88256200-88297600	Weak transcription	Right Ventricle	heart
6	chr6:88256400-88295800	Weak transcription	Gastric	stomach
7	chr6:88263400-88291400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:88264600-88291000	Weak transcription	Brain Angular Gyrus	brain
9	chr6:88269600-88291400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:88272200-88297000	Weak transcription	Brain Germinal Matrix	brain
11	chr6:88272400-88291000	Weak transcription	Fetal Brain Female	brain
12	chr6:88272400-88296000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:88272400-88297400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:88272400-88297400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:88272600-88291200	Weak transcription	HSMMtube	muscle
16	chr6:88272600-88292000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:88272800-88291000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:88273000-88292000	Weak transcription	Colonic Mucosa	Colon
19	chr6:88273000-88296000	Weak transcription	Brain Substantia Nigra	brain
20	chr6:88273600-88292400	Weak transcription	Hela-S3	cervix
21	chr6:88273600-88298200	Weak transcription	Fetal Kidney	kidney
22	chr6:88274000-88290800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:88274200-88295000	Weak transcription	NHLF	lung
24	chr6:88274400-88292200	Weak transcription	Fetal Lung	lung
25	chr6:88274800-88298800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:88278800-88290600	Weak transcription	HSMM	muscle
27	chr6:88278800-88297400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:88279600-88291000	Weak transcription	Placenta	Placenta
29	chr6:88282000-88292200	Weak transcription	NHEK	skin
30	chr6:88283000-88292200	Weak transcription	Ovary	ovary
31	chr6:88283000-88296600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:88283000-88297000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:88283000-88298600	Weak transcription	Aorta	Aorta
34	chr6:88284400-88291400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:88284400-88291600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:88284400-88293800	Weak transcription	Small Intestine	intestine
37	chr6:88284400-88298000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:88284800-88298200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr6:88285200-88293600	Weak transcription	Fetal Heart	heart
40	chr6:88285200-88297400	Weak transcription	Brain Anterior Caudate	brain
41	chr6:88285400-88290600	Weak transcription	Colon Smooth Muscle	Colon
42	chr6:88285400-88291000	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr6:88285400-88291000	Weak transcription	Left Ventricle	heart
44	chr6:88285400-88293800	Weak transcription	Brain Hippocampus Middle	brain
45	chr6:88285400-88295600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr6:88285400-88297200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr6:88285400-88297600	Weak transcription	Pancreas	Pancrea
48	chr6:88285600-88290600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:88285600-88291000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:88285600-88291200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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