Variant report

Variant	rs7133378
Chromosome Location	chr12:124409502-124409503
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:124407933..124410247-chr12:124410271..124413252,2	MCF-7	breast:
2	chr12:124408910..124411445-chr12:124416040..124418769,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197653	Chromatin interaction
ENSG00000270028	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1054852	0.83[ASW][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs10846577	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs10846578	1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs10846579	0.92[CEU][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10846580	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057393	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057394	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11057396	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057397	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11057399	0.85[EUR][1000 genomes]
rs11057401	0.84[CEU][hapmap];0.86[GIH][hapmap]
rs11057408	0.92[CEU][hapmap];0.96[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs11057409	0.92[CEU][hapmap];0.96[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs11057412	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs11057413	0.84[EUR][1000 genomes]
rs11831913	0.84[CEU][hapmap]
rs11833002	0.86[EUR][1000 genomes]
rs11835839	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11837287	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs1187415	0.92[CEU][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs12296259	0.87[EUR][1000 genomes]
rs12298484	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12301673	0.85[EUR][1000 genomes]
rs12303671	0.92[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs12303933	0.83[EUR][1000 genomes]
rs12309481	0.89[YRI][hapmap]
rs12310367	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs12311114	0.84[CEU][hapmap];0.86[GIH][hapmap]
rs12311848	0.83[EUR][1000 genomes]
rs12316080	0.85[EUR][1000 genomes]
rs12317176	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12322694	0.82[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs12809125	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12809473	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs12823740	1.00[ASW][hapmap];0.92[CEU][hapmap];0.96[GIH][hapmap];0.81[LWK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap]
rs12824567	0.84[CEU][hapmap]
rs12827409	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs12829951	0.85[EUR][1000 genomes]
rs12833624	0.84[EUR][1000 genomes]
rs2130382	0.84[CEU][hapmap]
rs2178663	0.84[CEU][hapmap];0.86[GIH][hapmap]
rs34114498	0.84[EUR][1000 genomes]
rs34878139	0.86[EUR][1000 genomes]
rs35099862	0.84[EUR][1000 genomes]
rs3789967	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3802999	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4405410	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4575361	0.96[ASN][1000 genomes]
rs4765127	0.92[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs4765148	0.84[CEU][hapmap];0.82[GIH][hapmap]
rs4765219	0.92[CEU][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs4765305	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4765528	0.84[CEU][hapmap];0.86[GIH][hapmap]
rs4765541	0.85[EUR][1000 genomes]
rs4765562	0.85[EUR][1000 genomes]
rs4930721	1.00[CHB][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.94[ASN][1000 genomes]
rs4930723	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs4930724	0.94[ASW][hapmap];0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4930725	0.85[EUR][1000 genomes]
rs4930726	0.92[CEU][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55990776	0.80[EUR][1000 genomes]
rs56041971	0.83[EUR][1000 genomes]
rs6488912	0.86[EUR][1000 genomes]
rs6488913	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs6488914	0.84[CEU][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap]
rs7131882	0.85[EUR][1000 genomes]
rs7132655	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs7134121	0.84[EUR][1000 genomes]
rs7135314	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs71458830	0.83[EUR][1000 genomes]
rs7301953	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7305864	0.92[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs7307053	0.84[CEU][hapmap];0.83[GIH][hapmap]
rs7307277	0.92[CEU][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs7311233	0.84[CEU][hapmap];0.86[GIH][hapmap]
rs7311969	0.94[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs7312404	0.92[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs7958691	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs7961449	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7966192	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7973683	0.94[ASW][hapmap];0.92[CEU][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7975482	0.92[CEU][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs7978610	0.92[CEU][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs952632	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs9863	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs9971695	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[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	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv1811815	chr12:124374716-124424636	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1832870	chr12:124374716-124424636	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv522321	chr12:124383950-124424636	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7133378	RP11-380L11.4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124393800-124418000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr12:124394200-124418400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:124400400-124417800	Weak transcription	Spleen	Spleen
4	chr12:124406200-124411800	Weak transcription	Brain Germinal Matrix	brain
5	chr12:124406800-124412400	Weak transcription	Thymus	Thymus
6	chr12:124407400-124422000	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr12:124408400-124418000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:124408800-124428000	Weak transcription	Right Atrium	heart
9	chr12:124409200-124414600	Weak transcription	Fetal Brain Female	brain
10	chr12:124409400-124410200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:124409400-124419600	Weak transcription	Right Ventricle	heart

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