Variant report

Variant	rs1877463
Chromosome Location	chr13:30147596-30147597
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:30145938..30148491-chr13:30169335..30172186,4	K562	blood:
2	chr13:30140340..30147664-chr13:30167192..30171255,11	MCF-7	breast:
3	chr13:30146852..30149367-chr13:30152203..30154425,2	MCF-7	breast:
4	chr13:30141734..30150637-chr13:30164575..30171336,12	MCF-7	breast:
5	chr13:30102776..30104828-chr13:30146774..30149345,2	K562	blood:
6	chr13:30147177..30149389-chr13:30151174..30153674,3	K562	blood:

Variant related genes	Relation type
ENSG00000139514	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1018679	0.89[CHB][hapmap]
rs11839516	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12428026	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs166828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150688	0.80[CHB][hapmap]
rs2150690	0.81[CHB][hapmap]
rs2236499	0.90[CHB][hapmap]
rs2277451	0.80[CHB][hapmap]
rs2802249	0.81[CHB][hapmap]
rs280922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280923	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs280924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280925	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280926	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280928	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs280930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280931	0.94[ASN][1000 genomes]
rs280933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280934	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs280936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2989594	0.81[CHB][hapmap]
rs3011605	0.81[CHB][hapmap]
rs3783257	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs3783259	0.81[CHB][hapmap]
rs3783260	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs3783262	0.81[CHB][hapmap]
rs3783263	0.81[CHB][hapmap]
rs3803266	0.85[CHB][hapmap]
rs3825536	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs476506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs485359	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532568	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs537151	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs579451	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs617892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490409	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs7338758	0.85[CHB][hapmap]
rs7991883	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7997827	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs819386	0.99[ASN][1000 genomes]
rs914362	0.81[CHB][hapmap];0.84[MEX][hapmap]
rs9550482	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs9551696	0.86[CHB][hapmap]
rs9551699	1.00[ASW][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.91[ASN][1000 genomes]
rs9551700	0.86[CHB][hapmap]
rs9551701	0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv979	chr13:30122254-30167821	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1877463	C13orf36	trans	brain	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30126000-30161400	Weak transcription	Primary B cells from cord blood	blood
2	chr13:30127600-30151400	Weak transcription	Aorta	Aorta
3	chr13:30127600-30156400	Weak transcription	Lung	lung
4	chr13:30127800-30147600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr13:30128000-30163600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr13:30128600-30161800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr13:30128800-30155800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr13:30128800-30168200	Weak transcription	Primary T cells from cord blood	blood
9	chr13:30131400-30147800	Weak transcription	Fetal Brain Female	brain
10	chr13:30131800-30147600	Weak transcription	GM12878-XiMat	blood
11	chr13:30137200-30151000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr13:30138600-30154000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr13:30138800-30155800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr13:30138800-30159800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr13:30140600-30149200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr13:30141200-30147600	Weak transcription	Small Intestine	intestine
17	chr13:30143200-30151200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr13:30143600-30148000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr13:30143600-30149400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr13:30144200-30147600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr13:30144200-30151200	Weak transcription	Fetal Stomach	stomach
22	chr13:30144400-30147600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr13:30144400-30152400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr13:30144400-30155600	Weak transcription	HMEC	breast
25	chr13:30144600-30154000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr13:30144800-30148600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr13:30144800-30150000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr13:30144800-30154000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr13:30145000-30150800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr13:30145000-30151000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr13:30145600-30147800	Enhancers	Left Ventricle	heart
32	chr13:30145600-30148200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr13:30146000-30148000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr13:30146000-30148200	Enhancers	Fetal Muscle Trunk	muscle
35	chr13:30146000-30148200	Enhancers	Gastric	stomach
36	chr13:30146000-30154000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr13:30146200-30147800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr13:30146200-30147800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr13:30146200-30147800	Enhancers	Right Atrium	heart
40	chr13:30146200-30147800	Enhancers	Right Ventricle	heart
41	chr13:30146200-30147800	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr13:30146200-30148200	Enhancers	Esophagus	oesophagus
43	chr13:30146200-30148400	Enhancers	Duodenum Mucosa	Duodenum
44	chr13:30146200-30149400	Enhancers	Pancreas	Pancrea
45	chr13:30146400-30147800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr13:30146400-30154000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr13:30146400-30155400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr13:30146600-30148200	Enhancers	Stomach Mucosa	stomach
49	chr13:30146600-30148400	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr13:30146600-30149200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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