Variant report

Variant	rs9304097
Chromosome Location	chr18:29070441-29070442
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:29068752..29071565-chr18:29076556..29079913,5	MCF-7	breast:
2	chr18:29070302..29073813-chr18:29076378..29079026,4	MCF-7	breast:
3	chr18:29070292..29073847-chr18:29075738..29079463,4	K562	blood:
4	chr18:29068168..29070784-chr18:29076048..29078147,2	K562	blood:

Variant related genes	Relation type
ENSG00000046604	Chromatin interaction
ENSG00000266521	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1031729	0.94[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs1350731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1460602	0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs17660585	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1824477	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1841396	0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2212617	0.85[ASN][1000 genomes]
rs2212618	0.94[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2219584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704050	0.86[CEU][hapmap];0.89[CHB][hapmap];0.88[ASN][1000 genomes]
rs2704051	0.91[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2704052	0.91[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2704053	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2704055	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2848677	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2848680	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2848681	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4799310	0.87[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4799573	0.94[ASN][1000 genomes]
rs6506927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7227343	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7227984	0.91[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7231288	0.93[ASN][1000 genomes]
rs7231553	0.93[ASN][1000 genomes]
rs7232282	0.94[ASN][1000 genomes]
rs7235272	0.93[ASN][1000 genomes]
rs7236324	0.94[ASN][1000 genomes]
rs7236469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7238729	0.96[ASN][1000 genomes]
rs7239805	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7240824	0.88[ASN][1000 genomes]
rs7240920	0.96[ASN][1000 genomes]
rs7241107	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73414280	0.93[ASN][1000 genomes]
rs73953901	0.94[ASN][1000 genomes]
rs9304098	0.86[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9304099	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9941421	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9945031	0.91[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9945420	0.83[ASN][1000 genomes]
rs9951843	1.00[ASN][1000 genomes]
rs9961910	0.90[ASN][1000 genomes]
rs9961920	0.94[ASN][1000 genomes]
rs9961925	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9962121	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9962318	0.94[ASN][1000 genomes]
rs9962333	0.83[ASN][1000 genomes]
rs9962423	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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
rs9304097	RP11-650P15.1	cis	Thyroid	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29065400-29071800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr18:29066600-29071000	Enhancers	Placenta Amnion	Placenta Amnion
3	chr18:29067600-29076800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr18:29068000-29072000	Enhancers	Hela-S3	cervix
5	chr18:29068200-29071000	Weak transcription	NH-A	brain
6	chr18:29068400-29071600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr18:29068400-29071600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr18:29069000-29071600	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr18:29069200-29072200	Enhancers	Stomach Mucosa	stomach
10	chr18:29069600-29073200	Weak transcription	Esophagus	oesophagus
11	chr18:29070000-29070600	Flanking Active TSS	GM12878-XiMat	blood
12	chr18:29070000-29070600	Flanking Active TSS	NHEK	skin
13	chr18:29070000-29071200	Enhancers	Fetal Intestine Small	intestine
14	chr18:29070200-29070600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr18:29070200-29070600	Flanking Active TSS	HMEC	breast
16	chr18:29070200-29071000	Enhancers	Fetal Intestine Large	intestine
17	chr18:29070200-29071600	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr18:29070400-29070600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr18:29070400-29071200	Enhancers	A549	lung

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