Variant report

Variant	rs11169588
Chromosome Location	chr12:51239270-51239271
allele	G/T
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	FOS	chr12:51239111-51239452	MCF10A-Er-Src	breast:	n/a	chr12:51239280-51239289 chr12:51239281-51239289 chr12:51239281-51239290 chr12:51239282-51239289
2	FOS	chr12:51239099-51239452	MCF10A-Er-Src	breast:	n/a	chr12:51239280-51239289 chr12:51239281-51239289 chr12:51239281-51239290 chr12:51239282-51239289
3	JUND	chr12:51238729-51239570	SK-N-SH	brain:	n/a	chr12:51239280-51239289 chr12:51239281-51239289 chr12:51239279-51239290 chr12:51239281-51239290 chr12:51239282-51239289
4	JUND	chr12:51239097-51239457	HepG2	liver:	n/a	chr12:51239280-51239289 chr12:51239281-51239289 chr12:51239279-51239290 chr12:51239281-51239290 chr12:51239282-51239289
5	FOS	chr12:51239114-51239465	MCF10A-Er-Src	breast:	n/a	chr12:51239280-51239289 chr12:51239281-51239289 chr12:51239281-51239290 chr12:51239282-51239289
6	STAT3	chr12:51239227-51239433	MCF10A-Er-Src	breast:	n/a	chr12:51239280-51239289 chr12:51239281-51239290 chr12:51239289-51239296
7	FOSL2	chr12:51239145-51239333	HepG2	liver:	n/a	chr12:51239280-51239289 chr12:51239281-51239289 chr12:51239281-51239290 chr12:51239282-51239289
8	STAT3	chr12:51239233-51239427	MCF10A-Er-Src	breast:	n/a	chr12:51239280-51239289 chr12:51239281-51239290 chr12:51239289-51239296
9	JUND	chr12:51239085-51239426	K562	blood:	n/a	chr12:51239280-51239289 chr12:51239281-51239289 chr12:51239279-51239290 chr12:51239281-51239290 chr12:51239282-51239289
10	JUN	chr12:51239164-51239416	HepG2	liver:	n/a	chr12:51239280-51239289 chr12:51239281-51239289 chr12:51239281-51239290 chr12:51239282-51239289
11	KAP1	chr12:51239126-51239631	U2OS	brain:	n/a	chr12:51239279-51239288
12	STAT3	chr12:51239101-51239420	MCF10A-Er-Src	breast:	n/a	chr12:51239280-51239289 chr12:51239281-51239290 chr12:51239289-51239296
13	FOS	chr12:51239099-51239477	MCF10A-Er-Src	breast:	n/a	chr12:51239280-51239289 chr12:51239281-51239289 chr12:51239281-51239290 chr12:51239282-51239289
14	STAT3	chr12:51239125-51239729	MCF10A-Er-Src	breast:	n/a	chr12:51239280-51239289 chr12:51239281-51239290 chr12:51239289-51239296
15	MYC	chr12:51239099-51239374	MCF10A-Er-Src	breast:	n/a	chr12:51239280-51239289
16	MYC	chr12:51239090-51239438	MCF10A-Er-Src	breast:	n/a	chr12:51239280-51239289
17	JUND	chr12:51239108-51239473	Hela-S3	cervix:	n/a	chr12:51239280-51239289 chr12:51239281-51239289 chr12:51239279-51239290 chr12:51239281-51239290 chr12:51239282-51239289

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51234605..51237036-chr12:51237344..51239459,2	K562	blood:
2	chr12:51230105..51232434-chr12:51237161..51239319,2	MCF-7	breast:

Variant related genes	Relation type
RN7SL519P	TF binding region
ENSG00000243075	Chromatin interaction
ENSG00000186452	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10160844	0.89[ASN][1000 genomes]
rs10459237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10459238	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10459239	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10747595	0.92[ASN][1000 genomes]
rs10747596	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10747597	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747599	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs10783393	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783395	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10783404	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783405	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10783406	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs10876099	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876100	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876105	0.90[ASN][1000 genomes]
rs10876115	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876119	0.91[ASN][1000 genomes]
rs1096030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1096031	0.91[ASN][1000 genomes]
rs1103441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11169587	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11169589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169592	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169602	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169603	0.88[ASN][1000 genomes]
rs11169608	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169609	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169610	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169612	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169614	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11495280	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11533636	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12578465	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12578466	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12581103	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1362964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1583697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1631348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1642997	0.91[ASN][1000 genomes]
rs1643004	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1659375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2554852	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2554854	0.93[ASN][1000 genomes]
rs3752667	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4483656	0.93[ASN][1000 genomes]
rs4542479	0.81[ASN][1000 genomes]
rs4768926	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768937	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4768938	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs4768939	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131969	0.81[ASN][1000 genomes]
rs73100855	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7979616	0.93[ASN][1000 genomes]
rs829120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829126	0.88[ASN][1000 genomes]
rs829128	0.87[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs829129	0.90[ASN][1000 genomes]
rs829131	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs829132	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs829139	0.90[ASN][1000 genomes]
rs829141	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs829142	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs829143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs829144	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs844175	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs860476	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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	67 gene(s)	inside rSNPs	diseases
2	nsv899078	chr12:51213433-51286750	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51237000-51244400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:51237000-51244400	Weak transcription	Gastric	stomach
3	chr12:51237200-51240800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:51237800-51246400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:51238800-51239600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:51238800-51239600	Enhancers	Fetal Intestine Large	intestine
7	chr12:51239000-51239600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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