Variant report

Variant	rs4339500
Chromosome Location	chr6:110511814-110511815
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:110506447..110509996-chr6:110510060..110514287,5	K562	blood:
2	chr6:110511080..110513805-chr6:110536717..110538803,2	K562	blood:
3	chr6:110511664..110513527-chr6:110524643..110526823,2	MCF-7	breast:
4	chr6:110499664..110503910-chr6:110507183..110512081,7	K562	blood:
5	chr6:110501410..110504350-chr6:110509414..110512574,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168438	Chromatin interaction
ENSG00000112290	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11153226	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11751590	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11757055	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12110744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12660119	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12660791	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12662013	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12665849	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12665858	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1462492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1462493	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2002630	0.88[ASN][1000 genomes]
rs4257894	0.84[ASW][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4299857	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4509164	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4945850	0.84[ASW][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4945851	0.92[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4947048	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4947051	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4947058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56122480	0.93[ASN][1000 genomes]
rs56135788	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56287427	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57983455	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60495849	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61020234	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6568633	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6568634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6913554	0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6915379	0.91[ASN][1000 genomes]
rs6918148	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6925392	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6926540	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6927667	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6927697	0.84[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6927722	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6928684	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6938106	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6938139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6938653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs719849	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73535810	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73535817	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73535821	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73535837	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73535838	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73537927	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73537938	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73537949	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7744828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7766850	0.88[ASN][1000 genomes]
rs9384735	0.80[ASN][1000 genomes]
rs9481045	0.85[ASN][1000 genomes]
rs9481047	0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9481048	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9487317	0.88[ASN][1000 genomes]
rs9487318	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9487319	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9487321	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[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
rs4339500	WASF1	cis	Artery Tibial	GTEx
rs4339500	WASF1	cis	Muscle Skeletal	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110502600-110515000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:110502600-110533200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:110502600-110536600	Weak transcription	Esophagus	oesophagus
4	chr6:110502800-110513800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:110502800-110533400	Weak transcription	HSMMtube	muscle
6	chr6:110503200-110514800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:110503200-110515000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:110503200-110531400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:110503200-110533400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:110503400-110512000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:110503400-110515000	Weak transcription	Placenta	Placenta
12	chr6:110503400-110515000	Weak transcription	NH-A	brain
13	chr6:110503400-110530600	Weak transcription	Fetal Kidney	kidney
14	chr6:110503400-110536600	Weak transcription	Gastric	stomach
15	chr6:110503600-110514400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr6:110503600-110514400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:110503600-110514400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:110503600-110515200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:110503800-110515400	Weak transcription	Fetal Intestine Large	intestine
20	chr6:110503800-110532800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:110503800-110533400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:110504200-110514400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:110504400-110514800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:110504400-110536600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:110504600-110513800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr6:110504600-110513800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr6:110504600-110514400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:110504600-110519400	Weak transcription	Fetal Intestine Small	intestine
29	chr6:110504600-110532400	Weak transcription	HMEC	breast
30	chr6:110504600-110536600	Weak transcription	Fetal Stomach	stomach
31	chr6:110504800-110512800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:110504800-110514200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:110504800-110514400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:110504800-110514400	Weak transcription	Fetal Thymus	thymus
35	chr6:110504800-110514800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr6:110504800-110531400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr6:110504800-110531600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:110504800-110531800	Weak transcription	Fetal Brain Male	brain
39	chr6:110504800-110533400	Weak transcription	Fetal Muscle Leg	muscle
40	chr6:110504800-110533400	Weak transcription	NHEK	skin
41	chr6:110504800-110536600	Weak transcription	Pancreas	Pancrea
42	chr6:110504800-110536600	Weak transcription	Spleen	Spleen
43	chr6:110505000-110512400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr6:110505000-110512400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:110505000-110514400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr6:110505000-110514800	Weak transcription	Fetal Brain Female	brain
47	chr6:110505000-110522200	Weak transcription	K562	blood
48	chr6:110505200-110528800	Weak transcription	NHLF	lung
49	chr6:110505400-110532600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr6:110505600-110515000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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