Variant report

Variant	rs12660119
Chromosome Location	chr6:110405670-110405671
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	chr6:110400293..110402395-chr6:110404111..110406019,2	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11153226	0.89[ASW][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs11751590	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11757055	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12110744	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12660791	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12662013	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12665849	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12665858	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1462490	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1462492	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1462493	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2002630	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4257894	0.89[ASW][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.89[ASN][1000 genomes]
rs4299857	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4339500	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4509164	0.89[ASW][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs4945850	0.89[ASW][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];0.93[ASN][1000 genomes]
rs4945851	0.87[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.89[ASN][1000 genomes]
rs4947048	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4947051	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4947058	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56122480	0.93[ASN][1000 genomes]
rs56135788	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56287427	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57983455	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60495849	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61020234	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6568633	0.87[ASN][1000 genomes]
rs6568634	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6912291	0.81[ASN][1000 genomes]
rs6913554	0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6915379	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6918148	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6925392	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6926540	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6927667	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6927697	0.89[ASW][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];0.90[ASN][1000 genomes]
rs6927722	0.94[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6928684	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6938106	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6938139	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6938653	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs719849	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73533834	0.89[ASN][1000 genomes]
rs73535810	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73535817	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73535821	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73535837	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73535838	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73537927	0.87[ASN][1000 genomes]
rs73537938	0.87[ASN][1000 genomes]
rs73537949	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7744828	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7747842	0.86[ASN][1000 genomes]
rs9372247	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9372248	0.85[ASN][1000 genomes]
rs9374156	0.89[ASN][1000 genomes]
rs9400359	0.89[ASN][1000 genomes]
rs9400360	0.89[ASN][1000 genomes]
rs9481047	1.00[JPT][hapmap]
rs9481048	1.00[JPT][hapmap]
rs9487318	1.00[JPT][hapmap]
rs9487319	1.00[JPT][hapmap]
rs9487321	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:27 , 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	nsv1017551	chr6:110385054-110413225	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1023185	chr6:110386197-110416868	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1029169	chr6:110389869-110413225	Weak transcription Enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv2757188	chr6:110389926-110504680	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	esv2759462	chr6:110389926-110504680	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	esv2763956	chr6:110394513-110413237	Weak transcription Enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv2761056	chr6:110394513-110415428	Enhancers Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv1017890	chr6:110394894-110416868	Enhancers Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv7954	chr6:110395986-110413365	Enhancers Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv33686	chr6:110396119-110413310	Weak transcription Enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv604487	chr6:110396540-110406212	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv604488	chr6:110396540-110406426	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv604489	chr6:110396540-110408904	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv604490	chr6:110396540-110411065	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv604491	chr6:110396540-110412259	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv1026085	chr6:110396676-110420721	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
18	nsv604492	chr6:110398923-110411065	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv604493	chr6:110398923-110412259	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv604494	chr6:110399223-110412259	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv604495	chr6:110399873-110412259	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv604496	chr6:110400783-110411065	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv604497	chr6:110401183-110411065	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv604498	chr6:110401183-110412259	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv604499	chr6:110401183-110420374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
26	nsv604500	chr6:110402895-110412259	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
27	esv2829867	chr6:110404180-110414749	Weak transcription Enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12660119	BEND3	cis	parietal	SCAN
rs12660119	WASF1	cis	Artery Tibial	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110397000-110412800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:110397000-110415400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:110402800-110414400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:110402800-110419800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:110404600-110406800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr6:110405000-110405800	Enhancers	Ovary	ovary
7	chr6:110405000-110405800	Enhancers	HepG2	liver
8	chr6:110405000-110406000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:110405200-110405800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:110405200-110405800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:110405200-110406000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr6:110405400-110405800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:110405400-110418000	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:110405600-110422800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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