Variant report

Variant	rs12636078
Chromosome Location	chr3:20105673-20105674
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20105530..20108149-chr3:20143893..20147714,3	MCF-7	breast:
2	chr3:20096569..20098445-chr3:20104189..20106827,2	MCF-7	breast:
3	chr3:19987687..19990266-chr3:20104517..20106901,2	K562	blood:
4	chr3:20102932..20104698-chr3:20105187..20107405,2	K562	blood:

Variant related genes	Relation type
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12636032	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12638247	0.87[ASN][1000 genomes]
rs2929394	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2948097	0.91[CHB][hapmap];0.90[ASN][1000 genomes]
rs4858767	0.80[JPT][hapmap]
rs6550351	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs6777429	0.89[ASN][1000 genomes]
rs6793122	0.84[YRI][hapmap]
rs7355958	0.86[JPT][hapmap];0.84[YRI][hapmap];0.87[ASN][1000 genomes]
rs7617840	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs7627847	0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7642107	0.92[ASN][1000 genomes]
rs9816216	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9817616	0.87[ASN][1000 genomes]
rs9874923	0.81[ASW][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.88[YRI][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12636078	RAB5A	cis	cerebellum	SCAN
rs12636078	KAT2B	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20096600-20106400	Weak transcription	Fetal Intestine Large	intestine
2	chr3:20097200-20106400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:20099000-20122600	Weak transcription	Aorta	Aorta
4	chr3:20099200-20106000	Weak transcription	Right Ventricle	heart
5	chr3:20099400-20105800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:20099400-20106400	Weak transcription	Ovary	ovary
7	chr3:20099400-20106600	Weak transcription	Pancreas	Pancrea
8	chr3:20099400-20108600	Weak transcription	Fetal Stomach	stomach
9	chr3:20099400-20112600	Weak transcription	HSMMtube	muscle
10	chr3:20099400-20112800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:20099400-20122600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:20099400-20122800	Weak transcription	Lung	lung
13	chr3:20099600-20106000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:20099800-20106600	Weak transcription	Spleen	Spleen
15	chr3:20100000-20109200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:20102800-20105800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:20102800-20106000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:20102800-20106400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:20102800-20113400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:20102800-20136800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:20103000-20106000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr3:20103000-20106000	Weak transcription	Right Atrium	heart
23	chr3:20103000-20106000	Weak transcription	Small Intestine	intestine
24	chr3:20103000-20106600	Weak transcription	Adipose Nuclei	Adipose
25	chr3:20103000-20106600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:20103000-20108400	Weak transcription	Fetal Thymus	thymus
27	chr3:20103000-20108400	Weak transcription	Osteobl	bone
28	chr3:20103000-20111400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:20103200-20105800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:20103200-20105800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:20103200-20105800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:20103200-20106000	Weak transcription	Brain Anterior Caudate	brain
33	chr3:20103200-20106400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:20103200-20106400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:20103200-20106400	Weak transcription	Fetal Lung	lung
36	chr3:20103200-20107600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr3:20103200-20108400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:20103200-20108400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:20103200-20108600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:20103200-20108600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:20103200-20108600	Weak transcription	NHDF-Ad	bronchial
42	chr3:20103200-20108800	Weak transcription	A549	lung
43	chr3:20103200-20110400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:20103200-20112600	Weak transcription	Primary T cells from cord blood	blood
45	chr3:20103200-20112800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr3:20103200-20113000	Weak transcription	Primary B cells from cord blood	blood
47	chr3:20103200-20113000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr3:20103200-20113000	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr3:20103200-20113200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr3:20103200-20114000	Weak transcription	Liver	Liver

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