Variant report

Variant	rs12612046
Chromosome Location	chr2:63209314-63209315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63168550..63170983-chr2:63208224..63209824,2	K562	blood:
2	chr2:63205690..63208666-chr2:63208773..63211322,2	K562	blood:

Variant related genes	Relation type
ENSG00000115504	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11125949	1.00[ASW][hapmap];0.83[GIH][hapmap];1.00[YRI][hapmap]
rs12473894	1.00[YRI][hapmap]
rs12613453	0.95[ASN][1000 genomes]
rs12614162	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17347994	1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17407696	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs17432559	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432566	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs17432580	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432615	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17473084	0.86[EUR][1000 genomes]
rs17598689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17598881	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671458	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs4671461	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv2756598	chr2:63085848-63491438	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	esv3340700	chr2:63127412-63534998	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12612046	PEX13	cis	cerebellum	SCAN
rs12612046	AFTPH	cis	cerebellum	SCAN
rs12612046	TMEM17	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63151400-63272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:63167600-63256000	Weak transcription	HSMMtube	muscle
3	chr2:63167800-63225800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr2:63168200-63220200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:63169600-63228800	Weak transcription	GM12878-XiMat	blood
6	chr2:63169800-63237000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr2:63170400-63255600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:63171400-63209800	Weak transcription	Brain Anterior Caudate	brain
9	chr2:63171800-63218600	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:63171800-63233000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:63173800-63225800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:63176200-63220200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:63177800-63226800	Weak transcription	Hela-S3	cervix
14	chr2:63179600-63219800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:63182000-63228800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:63182600-63215800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:63183400-63218600	Weak transcription	Brain Substantia Nigra	brain
18	chr2:63190400-63228800	Weak transcription	Gastric	stomach
19	chr2:63194600-63216000	Weak transcription	Fetal Brain Male	brain
20	chr2:63194600-63223600	Weak transcription	K562	blood
21	chr2:63194600-63223800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:63197200-63225400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:63197600-63234800	Strong transcription	HepG2	liver
24	chr2:63197800-63227800	Strong transcription	Liver	Liver
25	chr2:63198000-63211600	Weak transcription	Fetal Heart	heart
26	chr2:63198800-63218800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:63199800-63258200	Weak transcription	Lung	lung
28	chr2:63200800-63239400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:63201400-63223800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:63203600-63225800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:63203800-63210800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr2:63204400-63210600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:63204600-63217800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr2:63204800-63225200	Weak transcription	Spleen	Spleen
35	chr2:63204800-63229800	Weak transcription	Thymus	Thymus
36	chr2:63205000-63223800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr2:63205000-63238200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr2:63205600-63209800	Strong transcription	NHEK	skin
39	chr2:63205600-63219200	Strong transcription	NHDF-Ad	bronchial
40	chr2:63205800-63209400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:63205800-63213600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:63205800-63232400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr2:63206000-63213200	Strong transcription	Adipose Nuclei	Adipose
44	chr2:63206000-63227200	Weak transcription	Right Ventricle	heart
45	chr2:63206200-63210000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:63206200-63210000	Strong transcription	Fetal Intestine Large	intestine
47	chr2:63206200-63210200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:63206200-63210200	Strong transcription	Primary T cells from cord blood	blood
49	chr2:63206200-63210200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:63206200-63210200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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