Variant report

Variant	rs9450732
Chromosome Location	chr6:88249826-88249827
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88240311..88242545-chr6:88248910..88250768,2	K562	blood:
2	chr6:88248391..88251882-chr6:88297586..88301251,3	MCF-7	breast:
3	chr6:88240458..88244227-chr6:88248910..88253061,5	K562	blood:

Variant related genes	Relation type
ENSG00000146282	Chromatin interaction
ENSG00000135336	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1051131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1051148	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10755484	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13193380	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13194003	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13214153	0.91[CHB][hapmap]
rs2207144	0.91[CHB][hapmap]
rs2207146	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs2246113	0.96[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs2268993	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs2268994	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs2273129	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs2284908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs2300906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2300909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2307379	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2325064	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2754248	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2754260	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2754262	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs2787893	0.93[CEU][hapmap];0.87[CHB][hapmap];0.96[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2787921	0.87[EUR][1000 genomes]
rs2787924	0.86[EUR][1000 genomes]
rs2787927	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs2814712	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3757368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4334949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4464759	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4498321	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4587138	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4587143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4706294	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4707373	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707374	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707376	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4707377	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4707379	0.80[JPT][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707382	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4707383	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6454630	0.82[CHB][hapmap]
rs6454631	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6454632	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6454636	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6454638	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6454640	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6454641	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6905947	0.91[CHB][hapmap]
rs6906769	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908386	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6914299	0.91[CHB][hapmap]
rs6916732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918909	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923230	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6923355	0.83[EUR][1000 genomes]
rs6928160	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6930600	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6931069	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6933587	0.91[CHB][hapmap]
rs6940150	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7741825	0.91[CHB][hapmap];0.96[JPT][hapmap];0.83[ASN][1000 genomes]
rs7742965	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7746465	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7750207	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7754350	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7755167	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7756225	0.81[ASN][1000 genomes]
rs7757636	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7757794	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7761814	1.00[CEU][hapmap];0.96[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes]
rs7762864	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772561	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7773906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9294379	0.91[CHB][hapmap]
rs9294381	0.91[CHB][hapmap]
rs9444504	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs9444512	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444519	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]
rs9444522	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444524	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444525	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9444526	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9444530	0.82[ASN][1000 genomes]
rs9450701	0.91[CHB][hapmap]
rs9450704	1.00[CEU][hapmap];0.96[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes]
rs9450712	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs9450723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450726	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450733	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450738	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450739	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450744	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450752	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450755	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450762	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs985764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[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	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
rs9450732	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs9450732	SLC35A1	cis	multi-tissue	Pritchard
rs9450732	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs9450732	C6orf166	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 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	chr6:88225000-88250800	Weak transcription	Stomach Mucosa	stomach
3	chr6:88227000-88250200	Weak transcription	Fetal Heart	heart
4	chr6:88227800-88298800	Weak transcription	Esophagus	oesophagus
5	chr6:88228400-88250200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:88228400-88298400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:88228600-88254000	Weak transcription	Gastric	stomach
8	chr6:88228600-88262800	Weak transcription	Small Intestine	intestine
9	chr6:88228600-88271400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:88228600-88285200	Weak transcription	Spleen	Spleen
11	chr6:88228800-88253800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:88228800-88269600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr6:88229400-88261600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:88229400-88271200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:88229600-88254000	Weak transcription	Brain Anterior Caudate	brain
16	chr6:88229600-88289000	Weak transcription	Lung	lung
17	chr6:88230000-88267000	Weak transcription	Brain Substantia Nigra	brain
18	chr6:88230400-88271200	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:88230600-88254400	Weak transcription	Psoas Muscle	Psoas
20	chr6:88230800-88250600	Weak transcription	HSMMtube	muscle
21	chr6:88230800-88261600	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:88231200-88262800	Weak transcription	Brain Angular Gyrus	brain
23	chr6:88231200-88264200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr6:88238800-88253200	Weak transcription	K562	blood
25	chr6:88239200-88250400	Weak transcription	HUVEC	blood vessel
26	chr6:88240000-88253800	Weak transcription	Right Ventricle	heart
27	chr6:88240200-88250200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:88240200-88254000	Weak transcription	Colonic Mucosa	Colon
29	chr6:88240600-88250400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr6:88240600-88254000	Weak transcription	Fetal Brain Female	brain
31	chr6:88240600-88268200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:88240800-88250200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr6:88240800-88250200	Weak transcription	NHEK	skin
34	chr6:88240800-88250400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:88242400-88254000	Weak transcription	NHLF	lung
36	chr6:88244600-88253400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr6:88244800-88250200	Weak transcription	Pancreas	Pancrea
38	chr6:88244800-88254000	Weak transcription	Left Ventricle	heart
39	chr6:88244800-88254400	Weak transcription	Aorta	Aorta
40	chr6:88246600-88252200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:88246600-88252200	Strong transcription	NHDF-Ad	bronchial
42	chr6:88246800-88251800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:88247000-88251800	Strong transcription	Fetal Intestine Large	intestine
44	chr6:88247200-88251000	Strong transcription	NH-A	brain
45	chr6:88248000-88250200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:88248000-88251200	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr6:88248000-88255200	Strong transcription	Osteobl	bone
48	chr6:88248200-88250000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr6:88248200-88251600	Strong transcription	Thymus	Thymus
50	chr6:88248200-88251800	Strong transcription	Fetal Muscle Leg	muscle

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