Variant report

Variant	rs13072457
Chromosome Location	chr3:53102389-53102390
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:53102327-53102447	MCF-7	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RFT1-3	chr3:53100873-53109103	NONHSAT089980

Variant related genes	Relation type
SERBP1P3	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10510761	1.00[CEU][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs11706035	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11707575	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11707780	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs11710292	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11710394	1.00[CEU][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs11710707	0.84[EUR][1000 genomes]
rs11711773	0.88[EUR][1000 genomes]
rs11712653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11713171	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11713206	0.84[EUR][1000 genomes]
rs11713290	0.84[EUR][1000 genomes]
rs11713859	0.87[EUR][1000 genomes]
rs11713926	0.89[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs11714037	0.84[EUR][1000 genomes]
rs11714876	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11714902	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717132	0.84[EUR][1000 genomes]
rs11717619	1.00[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs11717715	0.84[EUR][1000 genomes]
rs11718388	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11718538	0.82[EUR][1000 genomes]
rs11718752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11718834	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11720191	0.84[EUR][1000 genomes]
rs13058817	0.87[EUR][1000 genomes]
rs13069006	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13072395	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13072818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13074524	0.84[EUR][1000 genomes]
rs13078834	0.84[EUR][1000 genomes]
rs13078971	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13084937	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13085514	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13085544	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13088281	1.00[ASW][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs13091844	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13092352	0.82[EUR][1000 genomes]
rs13320044	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1346719	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs1560333	1.00[JPT][hapmap]
rs17052727	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2336540	0.84[EUR][1000 genomes]
rs2336541	0.84[EUR][1000 genomes]
rs2564926	0.98[EUR][1000 genomes]
rs2581807	0.98[EUR][1000 genomes]
rs3097417	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34121720	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34238610	0.89[EUR][1000 genomes]
rs34244302	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34313969	0.84[EUR][1000 genomes]
rs34340609	0.94[EUR][1000 genomes]
rs34493168	0.84[EUR][1000 genomes]
rs34754279	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34872575	0.84[EUR][1000 genomes]
rs34933390	0.84[EUR][1000 genomes]
rs34943350	0.84[EUR][1000 genomes]
rs34979715	0.89[EUR][1000 genomes]
rs35076015	0.89[EUR][1000 genomes]
rs35163227	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35174175	0.89[EUR][1000 genomes]
rs35378159	0.84[EUR][1000 genomes]
rs35384050	0.84[EUR][1000 genomes]
rs35385050	0.84[EUR][1000 genomes]
rs35507120	0.89[EUR][1000 genomes]
rs35720014	0.84[EUR][1000 genomes]
rs35737577	0.84[EUR][1000 genomes]
rs35849389	0.84[EUR][1000 genomes]
rs36090694	0.84[EUR][1000 genomes]
rs3733034	0.83[GIH][hapmap]
rs3796352	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs3806692	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs3821872	0.91[EUR][1000 genomes]
rs4478072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58515094	0.84[EUR][1000 genomes]
rs58660500	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59583591	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60887045	0.84[EUR][1000 genomes]
rs60942590	0.84[EUR][1000 genomes]
rs61172708	0.84[EUR][1000 genomes]
rs6445555	0.86[EUR][1000 genomes]
rs6445556	0.93[EUR][1000 genomes]
rs6445557	0.93[EUR][1000 genomes]
rs71301804	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71301808	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71301809	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71301811	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71301814	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71301816	0.84[ASN][1000 genomes]
rs71617204	0.89[EUR][1000 genomes]
rs750474	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs7622420	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7625448	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7640293	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7645611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9756317	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs9875573	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13072457	TMEM110	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53098400-53106000	Weak transcription	Spleen	Spleen
2	chr3:53100200-53103600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:53100400-53105800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:53100600-53106000	Weak transcription	Primary T cells from cord blood	blood
5	chr3:53100800-53103600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:53101200-53103200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:53101400-53102400	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr3:53101400-53102400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr3:53102000-53103600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:53102200-53102600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:53102200-53105800	Weak transcription	Fetal Intestine Small	intestine
12	chr3:53102200-53105800	Weak transcription	K562	blood
13	chr3:53102200-53106000	Weak transcription	Fetal Intestine Large	intestine
14	chr3:53102200-53106400	Weak transcription	Colonic Mucosa	Colon

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