Variant report

Variant	rs12662099
Chromosome Location	chr6:110520202-110520203
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12660108	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12662027	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12662559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12664024	0.87[EUR][1000 genomes]
rs12664697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665152	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12665650	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1350943	0.87[EUR][1000 genomes]
rs1350944	0.87[EUR][1000 genomes]
rs1381688	0.87[EUR][1000 genomes]
rs2002631	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2361500	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2885293	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3806158	0.88[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3828928	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41288574	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41288576	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57771959	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58100980	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58965432	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59181827	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60105161	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61494781	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6904509	0.84[ASN][1000 genomes]
rs6918158	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6922245	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6922536	0.87[EUR][1000 genomes]
rs6926993	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6927464	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6935544	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6937364	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6940347	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6941101	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73765657	0.87[EUR][1000 genomes]
rs73765660	0.87[EUR][1000 genomes]
rs73765665	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7752069	0.87[EUR][1000 genomes]
rs7770634	0.87[EUR][1000 genomes]
rs7771649	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7771909	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9374151	0.87[EUR][1000 genomes]
rs9374153	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9374154	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9374155	0.87[EUR][1000 genomes]
rs9374157	0.87[EUR][1000 genomes]
rs9386877	0.87[EUR][1000 genomes]
rs9386879	0.87[EUR][1000 genomes]
rs9400361	0.87[EUR][1000 genomes]
rs9487320	0.81[ASN][1000 genomes]
rs9487324	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[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	nsv886535	chr6:110377006-110551463	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	esv1792799	chr6:110411065-110566597	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS 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 miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv948824	chr6:110443685-110889332	Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv1801843	chr6:110506109-110566328	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12662099	WASF1	cis	Nerve Tibial	GTEx
rs12662099	WASF1	cis	Artery Tibial	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110502600-110533200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:110502600-110536600	Weak transcription	Esophagus	oesophagus
3	chr6:110502800-110533400	Weak transcription	HSMMtube	muscle
4	chr6:110503200-110531400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:110503200-110533400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:110503400-110530600	Weak transcription	Fetal Kidney	kidney
7	chr6:110503400-110536600	Weak transcription	Gastric	stomach
8	chr6:110503800-110532800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:110503800-110533400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:110504400-110536600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:110504600-110532400	Weak transcription	HMEC	breast
12	chr6:110504600-110536600	Weak transcription	Fetal Stomach	stomach
13	chr6:110504800-110531400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:110504800-110531600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:110504800-110531800	Weak transcription	Fetal Brain Male	brain
16	chr6:110504800-110533400	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:110504800-110533400	Weak transcription	NHEK	skin
18	chr6:110504800-110536600	Weak transcription	Pancreas	Pancrea
19	chr6:110504800-110536600	Weak transcription	Spleen	Spleen
20	chr6:110505000-110522200	Weak transcription	K562	blood
21	chr6:110505200-110528800	Weak transcription	NHLF	lung
22	chr6:110505400-110532600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:110505600-110532200	Weak transcription	Hela-S3	cervix
24	chr6:110506000-110528800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:110506000-110532800	Weak transcription	Brain Substantia Nigra	brain
26	chr6:110507400-110536600	Weak transcription	Thymus	Thymus
27	chr6:110507600-110532800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr6:110507600-110533400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:110508400-110532800	Weak transcription	HepG2	liver
30	chr6:110510200-110531400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:110510400-110528800	Weak transcription	Osteobl	bone
32	chr6:110510600-110528800	Weak transcription	NHDF-Ad	bronchial
33	chr6:110511200-110524800	Weak transcription	GM12878-XiMat	blood
34	chr6:110512200-110536600	Weak transcription	Lung	lung
35	chr6:110512200-110538200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:110512200-110551000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:110512200-110552200	Weak transcription	Right Ventricle	heart
38	chr6:110512600-110528800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr6:110512600-110531400	Weak transcription	Brain Hippocampus Middle	brain
40	chr6:110512600-110533400	Weak transcription	Ovary	ovary
41	chr6:110512800-110533400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr6:110513000-110529200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:110513000-110533400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:110513000-110533400	Weak transcription	Left Ventricle	heart
45	chr6:110513000-110533400	Weak transcription	Psoas Muscle	Psoas
46	chr6:110513400-110532400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:110513400-110533200	Weak transcription	Brain Anterior Caudate	brain
48	chr6:110513400-110538600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr6:110513600-110528800	Weak transcription	Primary T cells from cord blood	blood
50	chr6:110513600-110528800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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