Variant report

Variant	rs7239805
Chromosome Location	chr18:29068068-29068069
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	chr18:29062010..29063666-chr18:29066941..29068808,2	K562	blood:
2	chr18:29066393..29069517-chr18:29071339..29073369,4	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1031729	0.85[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1350731	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1460602	0.85[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs17660585	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1824477	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1841396	0.85[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2212618	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2219584	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2704050	0.90[CHD][hapmap];0.91[MEX][hapmap];0.81[ASN][1000 genomes]
rs2704051	0.85[CEU][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.83[ASN][1000 genomes]
rs2704052	0.85[CEU][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.84[ASN][1000 genomes]
rs2704053	0.84[ASN][1000 genomes]
rs2848677	0.84[ASN][1000 genomes]
rs2848680	0.84[ASN][1000 genomes]
rs2848681	0.84[ASN][1000 genomes]
rs4799310	0.81[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4799573	0.86[ASN][1000 genomes]
rs6506927	0.89[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6506928	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7227343	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7227984	0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7231288	0.84[ASN][1000 genomes]
rs7231553	0.84[ASN][1000 genomes]
rs7232282	0.86[ASN][1000 genomes]
rs7235272	0.84[ASN][1000 genomes]
rs7236324	0.86[ASN][1000 genomes]
rs7236469	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7238729	0.87[ASN][1000 genomes]
rs7240824	0.80[ASN][1000 genomes]
rs7240920	0.95[ASN][1000 genomes]
rs7241107	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73414280	0.85[ASN][1000 genomes]
rs73953901	0.86[ASN][1000 genomes]
rs9304097	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9304098	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs9304099	0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9941421	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9945031	0.85[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9951843	0.91[ASN][1000 genomes]
rs9961910	0.82[ASN][1000 genomes]
rs9961920	0.86[ASN][1000 genomes]
rs9961925	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9962121	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9962318	0.86[ASN][1000 genomes]
rs9962423	0.93[EUR][1000 genomes];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	nsv1066692	chr18:28856066-29190505	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543674	chr18:28856066-29190505	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv916545	chr18:28898800-29166364	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833615	chr18:29008396-29192976	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7239805	RP11-650P15.1	cis	Thyroid	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29064400-29069000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr18:29065400-29071800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr18:29065600-29068400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr18:29065600-29070200	Enhancers	HMEC	breast
5	chr18:29066400-29068400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr18:29066600-29071000	Enhancers	Placenta Amnion	Placenta Amnion
7	chr18:29066800-29068200	Enhancers	A549	lung
8	chr18:29067000-29068400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr18:29067000-29068400	Enhancers	Ovary	ovary
10	chr18:29067200-29068200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr18:29067200-29068200	Enhancers	NH-A	brain
12	chr18:29067400-29068200	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr18:29067600-29076800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr18:29068000-29068200	Flanking Active TSS	NHEK	skin
15	chr18:29068000-29068400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr18:29068000-29069000	Weak transcription	Esophagus	oesophagus
17	chr18:29068000-29069000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr18:29068000-29070200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr18:29068000-29070400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr18:29068000-29072000	Enhancers	Hela-S3	cervix

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