Variant report

Variant	rs10929740
Chromosome Location	chr2:11572906-11572907
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11572499..11575442-chr2:11621165..11623225,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10186511	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10192676	0.82[JPT][hapmap]
rs10929736	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10929737	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10929739	1.00[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10929742	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11674593	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11680919	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11682602	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11685543	0.83[ASN][1000 genomes]
rs11686138	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11687178	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11687681	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691211	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11693023	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11694857	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12472962	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12611958	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12612948	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12613503	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12614218	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12615138	0.84[EUR][1000 genomes]
rs12615317	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12617534	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12988106	0.81[ASN][1000 genomes]
rs12990560	0.96[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12994661	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12995996	0.95[CEU][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13007909	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1369500	0.82[JPT][hapmap]
rs34079430	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34313955	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34514099	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35053846	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35306821	0.92[ASN][1000 genomes]
rs35423645	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35727311	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35818376	0.83[ASN][1000 genomes]
rs3922995	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4292073	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4335920	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4553788	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4588159	0.95[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57197575	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61016299	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6432192	0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6432193	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6432196	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6708001	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6708015	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6724463	0.82[JPT][hapmap]
rs6729114	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6735687	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6735707	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6736199	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6750266	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6750482	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6750499	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6751915	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7425786	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7556984	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7584175	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7595697	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9789694	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10929740	ITGB1BP1	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11546600-11584200	Weak transcription	Pancreas	Pancrea
2	chr2:11560400-11584000	Weak transcription	Aorta	Aorta
3	chr2:11560600-11576800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:11561200-11579200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:11561600-11575400	Weak transcription	Fetal Heart	heart
6	chr2:11562200-11573800	Weak transcription	A549	lung
7	chr2:11562800-11582400	Weak transcription	Left Ventricle	heart
8	chr2:11563000-11583800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:11563000-11586800	Weak transcription	Psoas Muscle	Psoas
10	chr2:11563400-11581600	Weak transcription	Adipose Nuclei	Adipose
11	chr2:11564200-11580000	Weak transcription	Ovary	ovary
12	chr2:11564600-11576400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:11565600-11578600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:11566600-11577800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:11567600-11573800	Weak transcription	Dnd41	blood
16	chr2:11567800-11577000	Weak transcription	HSMM	muscle
17	chr2:11569000-11578200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:11569600-11581800	Weak transcription	HepG2	liver
19	chr2:11570800-11576200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:11570800-11577800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:11571200-11582600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:11571200-11582800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:11571400-11580000	Weak transcription	HSMMtube	muscle
24	chr2:11571400-11581800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:11571600-11574800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:11571600-11580000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:11571800-11577400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:11571800-11581600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:11572000-11574200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:11572000-11575200	Weak transcription	NHEK	skin
31	chr2:11572000-11575400	Weak transcription	HMEC	breast
32	chr2:11572200-11576400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:11572400-11580000	Weak transcription	Gastric	stomach
34	chr2:11572400-11583800	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:11572600-11578400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:11572600-11588600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr2:11572800-11573000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
38	chr2:11572800-11578000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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