Variant report

Variant	rs11169567
Chromosome Location	chr12:51204938-51204939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51203453..51205584-chr12:51379862..51382375,2	MCF-7	breast:
2	chr12:51179438..51182295-chr12:51203599..51205649,2	MCF-7	breast:
3	chr12:51202962..51206871-chr12:51207911..51210941,4	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10783387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876084	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876087	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876092	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11169506	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs11169523	0.83[CHB][hapmap]
rs11169524	0.95[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap]
rs11169562	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169563	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169570	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169572	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169578	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]
rs1129406	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11503907	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12372718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12427378	0.83[CHB][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap]
rs12818741	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1316607	0.83[CHB][hapmap];0.93[TSI][hapmap]
rs13378012	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs2090852	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2139930	0.95[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap]
rs2280503	0.95[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs34645899	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34863430	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35353300	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742062	0.95[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs4307773	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs4388959	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs4768903	0.82[TSI][hapmap]
rs4986838	0.94[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61926301	0.88[EUR][1000 genomes]
rs61926303	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7133974	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7137845	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs7297504	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7304335	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7306677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974517	0.86[EUR][1000 genomes]
rs864899	0.92[CEU][hapmap]
rs876080	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs9943712	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[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	nsv976745	chr12:51203441-51215185	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11169567	DIP2B	cis	cerebellum	SCAN
rs11169567	ATF1	cis	Esophagus Muscularis	GTEx
rs11169567	KIAA1463	cis	multi-tissue	Pritchard
rs11169567	DIP2B	cis	multi-tissue	Pritchard
rs11169567	LASS5	cis	parietal	SCAN
rs11169567	ATF1	cis	Artery Tibial	GTEx
rs11169567	LASS5	cis	multi-tissue	Pritchard
rs11169567	ATF1	cis	Adipose Subcutaneous	GTEx
rs11169567	KRT73	cis	parietal	SCAN
rs11169567	EPLIN	cis	multi-tissue	Pritchard
rs11169567	CERS5	cis	Nerve Tibial	GTEx
rs11169567	FAIM2	cis	cerebellum	SCAN
rs11169567	DIP2B	cis	Lymphoblastoid	GTEx
rs11169567	LASS5	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51188600-51207800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:51190200-51215200	Weak transcription	Pancreas	Pancrea
3	chr12:51193200-51207600	Weak transcription	Fetal Heart	heart
4	chr12:51193200-51207800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:51193200-51207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:51193200-51207800	Weak transcription	Esophagus	oesophagus
7	chr12:51193200-51208000	Weak transcription	Small Intestine	intestine
8	chr12:51193200-51211200	Weak transcription	Aorta	Aorta
9	chr12:51193400-51207800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:51194400-51207800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:51194600-51207800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:51194600-51214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:51194800-51209200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:51198600-51215400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr12:51199600-51209400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:51200400-51209200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:51200600-51222200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:51201400-51206600	Strong transcription	Dnd41	blood
19	chr12:51201400-51213800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:51201600-51212400	Strong transcription	Fetal Lung	lung
21	chr12:51201600-51213200	Strong transcription	Fetal Muscle Leg	muscle
22	chr12:51201800-51205800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:51201800-51212200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:51201800-51212200	Strong transcription	Fetal Intestine Large	intestine
25	chr12:51201800-51212400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:51201800-51213800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:51202000-51206000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:51202000-51206200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:51202000-51213000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:51202000-51213200	Strong transcription	Fetal Stomach	stomach
31	chr12:51202200-51205200	Strong transcription	HepG2	liver
32	chr12:51202200-51206600	Strong transcription	Thymus	Thymus
33	chr12:51202200-51213200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:51202200-51213200	Strong transcription	Fetal Intestine Small	intestine
35	chr12:51202200-51213800	Strong transcription	Fetal Thymus	thymus
36	chr12:51202200-51214200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:51202400-51206800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:51202600-51213800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:51202600-51214400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr12:51202800-51205000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:51202800-51206000	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr12:51202800-51206000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr12:51202800-51208600	Strong transcription	Hela-S3	cervix
44	chr12:51202800-51213600	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr12:51202800-51214000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:51202800-51215000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:51203000-51206600	Strong transcription	Placenta	Placenta
48	chr12:51203000-51206800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:51203200-51205000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:51203200-51205000	Strong transcription	Colonic Mucosa	Colon

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