Variant report

Variant	rs13062734
Chromosome Location	chr3:105513689-105513690
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	chr3:105504771..105508747-chr3:105511531..105514547,3	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10490830	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11706886	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs11929289	0.92[ASN][1000 genomes]
rs13061160	0.86[ASN][1000 genomes]
rs13065142	0.84[ASN][1000 genomes]
rs13070917	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs13073784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13082334	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13093260	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs1443105	0.92[CHB][hapmap]
rs1867189	0.92[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs1867190	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs2120585	0.86[CHB][hapmap]
rs2301029	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs2301032	0.87[ASN][1000 genomes]
rs2399055	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs34896116	0.85[ASN][1000 genomes]
rs35581896	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3732554	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3772513	0.93[CHD][hapmap];0.92[ASN][1000 genomes]
rs3772521	0.86[CHB][hapmap];0.88[ASN][1000 genomes]
rs3772536	0.86[CHB][hapmap]
rs3772537	0.86[CHB][hapmap]
rs4321559	0.92[ASN][1000 genomes]
rs6437614	0.92[ASN][1000 genomes]
rs6780015	1.00[ASW][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes]
rs6796643	0.92[ASN][1000 genomes]
rs726444	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs7615317	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7619647	0.92[CHB][hapmap];0.97[CHD][hapmap];0.92[ASN][1000 genomes]
rs7624530	0.92[CHB][hapmap]
rs7649520	0.92[ASN][1000 genomes]
rs894937	0.85[ASN][1000 genomes]
rs9870097	0.84[CHB][hapmap]
rs9872897	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs999046	0.92[CHB][hapmap]

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	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13062734	CBLB	cis	multi-tissue	Pritchard
rs13062734	CBLB	Cis_1M	lymphoblastoid	RTeQTL
rs13062734	CCDC54	cis	cerebellum	SCAN
rs13062734	CHI3L2	trans	lymphoblastoid	seeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105482800-105517400	Weak transcription	Fetal Intestine Large	intestine
2	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
3	chr3:105486800-105519000	Weak transcription	Esophagus	oesophagus
4	chr3:105489600-105525400	Weak transcription	Fetal Intestine Small	intestine
5	chr3:105494400-105516200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:105495400-105517200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:105496400-105514000	Weak transcription	Lung	lung
8	chr3:105501800-105516600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:105505000-105527800	Weak transcription	Pancreas	Pancrea
10	chr3:105505000-105548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:105505600-105517400	Weak transcription	Brain Substantia Nigra	brain
12	chr3:105506200-105516000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:105506600-105518200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:105509000-105515000	Weak transcription	Fetal Kidney	kidney
15	chr3:105509200-105513800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:105509200-105514000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr3:105509800-105527800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:105510000-105517400	Weak transcription	Stomach Mucosa	stomach
19	chr3:105510200-105516400	Weak transcription	Primary T cells from cord blood	blood
20	chr3:105510600-105521200	Weak transcription	Fetal Brain Male	brain
21	chr3:105511400-105513800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
23	chr3:105511600-105515200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr3:105511600-105516600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:105511600-105516800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:105511800-105520400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:105512000-105514200	Weak transcription	GM12878-XiMat	blood
28	chr3:105512000-105515000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:105512000-105516800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:105512000-105516800	Weak transcription	NH-A	brain
31	chr3:105512000-105520600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:105512200-105513800	Enhancers	NHDF-Ad	bronchial
33	chr3:105512200-105514400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr3:105512200-105514800	Weak transcription	Primary B cells from cord blood	blood
35	chr3:105512200-105515000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:105512200-105516200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:105512200-105516200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:105512200-105516600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:105512200-105517200	Weak transcription	Fetal Lung	lung
40	chr3:105512200-105517400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:105512200-105517400	Weak transcription	Fetal Heart	heart
42	chr3:105512200-105517400	Weak transcription	Ovary	ovary
43	chr3:105512200-105517400	Weak transcription	Small Intestine	intestine
44	chr3:105512200-105519000	Weak transcription	Psoas Muscle	Psoas
45	chr3:105512200-105519000	Weak transcription	Right Atrium	heart
46	chr3:105512200-105519200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:105512200-105520200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:105512200-105520400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:105512200-105527200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:105512200-105534200	Weak transcription	Left Ventricle	heart

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