Variant report

Variant	rs11169587
Chromosome Location	chr12:51238989-51238990
allele	C/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	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

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: 4 )

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

rs_ID	r²[population]
rs10160844	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10459237	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10459238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10459239	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747595	0.83[ASN][1000 genomes]
rs10747596	0.82[ASN][1000 genomes]
rs10747597	0.89[ASN][1000 genomes]
rs10747599	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10783393	0.88[ASN][1000 genomes]
rs10783394	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10783395	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783404	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10783405	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap]
rs10783406	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876099	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs10876100	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs10876105	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876115	0.85[ASN][1000 genomes]
rs10876119	0.83[ASN][1000 genomes]
rs1096030	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1096031	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1103441	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169588	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11169589	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11169592	0.89[ASN][1000 genomes]
rs11169593	0.87[EUR][1000 genomes]
rs11169602	0.85[ASN][1000 genomes]
rs11169603	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169608	0.85[ASN][1000 genomes]
rs11169609	0.85[ASN][1000 genomes]
rs11169610	0.85[ASN][1000 genomes]
rs11169612	0.85[ASN][1000 genomes]
rs11169614	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11495280	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11533636	0.83[ASN][1000 genomes]
rs12578465	0.83[ASN][1000 genomes]
rs12578466	0.83[ASN][1000 genomes]
rs12581103	0.91[ASN][1000 genomes]
rs1362964	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1583697	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1631348	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1642997	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1643004	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1659375	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs2554852	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2554854	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2579077	0.95[CEU][hapmap]
rs3752667	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4483656	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768926	0.87[ASN][1000 genomes]
rs4768937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768938	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768939	0.91[ASN][1000 genomes]
rs73100855	0.88[ASN][1000 genomes]
rs7979616	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs829120	1.00[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs829122	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs829126	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829128	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829129	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829131	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap]
rs829132	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs829139	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829141	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829142	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829143	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs829144	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs844175	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs860476	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11169587	TUBA1B	cis	cerebellum	SCAN
rs11169587	RHEBL1	cis	cerebellum	SCAN
rs11169587	KRT79	cis	cerebellum	SCAN
rs11169587	LASS5	cis	cerebellum	SCAN

Chromatin state (count:10 , 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	chr12:51237200-51239000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:51237200-51240800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:51237400-51239200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:51237800-51246400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:51238800-51239000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:51238800-51239200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:51238800-51239600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:51238800-51239600	Enhancers	Fetal Intestine Large	intestine

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