Variant report

Variant	rs11169578
Chromosome Location	chr12:51219701-51219702
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51212786..51214358-chr12:51219133..51221117,2	K562	blood:
2	chr12:51218257..51221554-chr12:51475850..51478812,3	MCF-7	breast:
3	chr12:51157232..51159790-chr12:51217662..51220370,4	MCF-7	breast:
4	chr12:51219126..51219822-chr12:51379841..51381362,5	MCF-7	breast:
5	chr12:51218827..51219730-chr12:51421603..51422600,3	MCF-7	breast:
6	chr12:51216774..51221510-chr12:51379576..51384198,5	MCF-7	breast:
7	chr12:51218193..51220790-chr12:51416290..51419028,2	K562	blood:
8	chr12:51218890..51219846-chr12:51380451..51381461,7	MCF-7	breast:
9	chr12:51219278..51219813-chr12:51735276..51735836,2	K562	blood:
10	chr12:51218097..51220673-chr12:51419291..51422139,4	MCF-7	breast:
11	chr12:51216775..51221102-chr12:51419333..51421670,3	K562	blood:
12	chr12:51219096..51220890-chr12:51222074..51224257,2	MCF-7	breast:
13	chr12:51184951..51187491-chr12:51218198..51219760,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10783387	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10876084	0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10876087	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10876092	0.84[EUR][1000 genomes]
rs10876098	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169524	0.89[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap]
rs11169562	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11169563	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11169567	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11169570	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169571	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169572	0.86[EUR][1000 genomes]
rs1129406	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11503907	0.81[AMR][1000 genomes]
rs12372718	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12427378	0.92[GIH][hapmap];0.93[TSI][hapmap]
rs12818741	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs1316607	0.93[TSI][hapmap]
rs13378012	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs2090852	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs2139930	0.89[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap]
rs2280503	0.89[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs34645899	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34863430	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35353300	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3742062	0.89[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs4307773	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs4388959	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs4768903	0.82[TSI][hapmap]
rs4986838	0.88[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61926303	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7133974	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7137845	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs7304335	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7306677	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs864899	0.92[CEU][hapmap]
rs876080	0.84[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap]
rs9943712	0.83[AMR][1000 genomes];0.81[EUR][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11169578	LASS5	cis	multi-tissue	Pritchard
rs11169578	DIP2B	cis	Lymphoblastoid	GTEx
rs11169578	DIP2B	cis	multi-tissue	Pritchard
rs11169578	KIAA1463	cis	multi-tissue	Pritchard
rs11169578	FAIM2	cis	cerebellum	SCAN
rs11169578	ATF1	cis	Artery Tibial	GTEx
rs11169578	ATF1	cis	Esophagus Muscularis	GTEx
rs11169578	LASS5	cis	parietal	SCAN
rs11169578	KRT73	cis	parietal	SCAN
rs11169578	LASS5	cis	cerebellum	SCAN
rs11169578	EPLIN	cis	multi-tissue	Pritchard
rs11169578	ATF1	cis	Adipose Subcutaneous	GTEx
rs11169578	DIP2B	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51200600-51222200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:51205000-51228200	Weak transcription	Gastric	stomach
3	chr12:51210200-51222000	Weak transcription	Esophagus	oesophagus
4	chr12:51210600-51222000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:51210600-51223400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:51211000-51222000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:51211000-51222000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:51213200-51222200	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:51213400-51221800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:51213400-51222600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:51213800-51222800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:51216200-51219800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:51217800-51220400	Weak transcription	Psoas Muscle	Psoas
14	chr12:51218800-51219800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:51218800-51219800	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr12:51218800-51220000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:51218800-51220000	Enhancers	Colon Smooth Muscle	Colon
18	chr12:51218800-51220200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:51218800-51220200	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr12:51218800-51223400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr12:51219000-51219800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:51219000-51220200	Enhancers	Rectal Smooth Muscle	rectum
23	chr12:51219200-51219800	Enhancers	Liver	Liver
24	chr12:51219200-51219800	Enhancers	HepG2	liver
25	chr12:51219200-51221800	Weak transcription	HMEC	breast
26	chr12:51219200-51223000	Weak transcription	Brain Anterior Caudate	brain
27	chr12:51219400-51220000	Enhancers	Fetal Stomach	stomach
28	chr12:51219400-51222400	Weak transcription	Brain Substantia Nigra	brain
29	chr12:51219600-51220200	Enhancers	Fetal Lung	lung
30	chr12:51219600-51222200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr12:51219600-51222400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr12:51219600-51222800	Weak transcription	Thymus	Thymus

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