Variant report

Variant	rs12617019
Chromosome Location	chr2:96905568-96905569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:96873776..96875796-chr2:96905403..96907728,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CIAO1-1	chr2:96905451-96906426	NONHSAT072550
2	lnc-CIAO1-1	chr2:96905451-96906426	ENSG00000204685.5

Variant related genes	Relation type
ENSG00000084090	Chromatin interaction
ENSG00000204685	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11551400	0.89[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs11886999	0.84[CEU][hapmap]
rs12613263	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12618133	0.94[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2276650	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3852673	1.00[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4371393	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4592891	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4826	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57476471	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59082429	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59664047	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60409279	0.81[EUR][1000 genomes]
rs62153010	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62153011	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62153014	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62153018	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62153020	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62153022	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62153029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6576968	0.83[CEU][hapmap];0.94[GIH][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap]
rs72825854	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72825856	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72825864	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72825877	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7579709	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7580178	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs997547	0.83[CEU][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap]
rs997548	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
9	nsv963665	chr2:96882253-96905611	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12617019	ANKRD36B	cis	cerebellum	SCAN
rs12617019	TMEM127	cis	cerebellum	SCAN
rs12617019	CIAO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96875000-96906200	Weak transcription	Esophagus	oesophagus
2	chr2:96875600-96907000	Weak transcription	Fetal Thymus	thymus
3	chr2:96875800-96905800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:96876000-96905800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:96876000-96906600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:96876000-96915200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:96876200-96906000	Weak transcription	Osteobl	bone
8	chr2:96876200-96906600	Weak transcription	Brain Anterior Caudate	brain
9	chr2:96876200-96916000	Weak transcription	Dnd41	blood
10	chr2:96876200-96917800	Weak transcription	Brain Angular Gyrus	brain
11	chr2:96877800-96916000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:96886000-96905600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:96887800-96905600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:96889600-96915800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:96891200-96916200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:96891400-96916400	Weak transcription	HSMM	muscle
17	chr2:96891600-96905600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr2:96891600-96906800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:96893200-96907600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:96896000-96906600	Weak transcription	Placenta	Placenta
21	chr2:96896000-96907800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:96896200-96917600	Weak transcription	Pancreas	Pancrea
23	chr2:96896600-96911200	Weak transcription	K562	blood
24	chr2:96897400-96906000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:96897400-96906000	Weak transcription	HMEC	breast
26	chr2:96897400-96906200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:96899600-96918800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:96900000-96907000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:96900000-96917800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:96900200-96906200	Weak transcription	Liver	Liver
31	chr2:96900200-96907800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:96900400-96906400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:96900400-96917600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:96900600-96907000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:96900800-96906600	Weak transcription	Primary B cells from cord blood	blood
36	chr2:96900800-96906600	Weak transcription	GM12878-XiMat	blood
37	chr2:96900800-96906800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr2:96901000-96905600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:96901200-96906000	Weak transcription	NHEK	skin
40	chr2:96901200-96907800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:96901200-96907800	Weak transcription	NHLF	lung
42	chr2:96901800-96914600	Weak transcription	Ovary	ovary
43	chr2:96902400-96905600	Enhancers	Duodenum Mucosa	Duodenum
44	chr2:96902600-96917600	Weak transcription	Fetal Lung	lung
45	chr2:96903200-96906800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:96903200-96907400	Strong transcription	Stomach Smooth Muscle	stomach
47	chr2:96903200-96910000	Strong transcription	Fetal Stomach	stomach
48	chr2:96903400-96905800	Weak transcription	Thymus	Thymus
49	chr2:96903400-96906400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:96903800-96907600	Weak transcription	Hela-S3	cervix

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