Variant report

Variant	rs11072729
Chromosome Location	chr15:78402001-78402002
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78292154..78293026-chr15:78401681..78402212,2	MCF-7	breast:
2	chr15:78367037..78369598-chr15:78400476..78402359,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10456	0.87[CEU][hapmap];0.85[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11072727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072728	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11639461	0.82[ASN][1000 genomes]
rs12440984	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs16969507	0.93[CHB][hapmap];0.86[CHD][hapmap]
rs16969508	0.93[CHB][hapmap];0.86[CHD][hapmap]
rs16969514	0.93[CHB][hapmap];0.86[CHD][hapmap]
rs1971151	0.86[CHB][hapmap]
rs2304829	0.82[CEU][hapmap];0.88[ASN][1000 genomes]
rs2867922	0.93[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs3784328	0.86[CHB][hapmap]
rs59999498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62009267	0.82[ASN][1000 genomes]
rs62009270	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62009271	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6495273	0.81[CEU][hapmap];0.85[ASN][1000 genomes]
rs7162025	0.85[ASN][1000 genomes]
rs7164338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72732564	0.82[ASN][1000 genomes]
rs7359294	0.86[CHB][hapmap]
rs8028859	0.85[ASN][1000 genomes]
rs8032449	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs8036417	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs9806257	0.81[EUR][1000 genomes];0.92[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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	esv274890	chr15:78396447-78402258	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11072729	CIB2	cis	Esophagus Mucosa	GTEx
rs11072729	CIB2	cis	multi-tissue	Pritchard
rs11072729	PPCDC	cis	cerebellum	SCAN
rs11072729	CIB2	cis	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78393200-78406000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78395000-78405600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:78395400-78405600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:78396000-78405400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:78396200-78405600	Weak transcription	Brain Anterior Caudate	brain
6	chr15:78396200-78421800	Weak transcription	Right Ventricle	heart
7	chr15:78396400-78404000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:78396400-78405400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr15:78396600-78405400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr15:78396600-78405600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:78396600-78423800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:78397000-78405600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:78397600-78421400	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:78398400-78405400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr15:78398400-78405600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:78398400-78423200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:78398600-78405200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:78398600-78405600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:78398600-78413200	Weak transcription	Spleen	Spleen
20	chr15:78398800-78406200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:78399000-78405400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:78400000-78412800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:78400000-78422400	Weak transcription	Brain Germinal Matrix	brain
24	chr15:78400200-78414600	Weak transcription	Fetal Brain Female	brain
25	chr15:78400800-78405200	Weak transcription	Osteobl	bone
26	chr15:78400800-78405400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr15:78400800-78405600	Weak transcription	HepG2	liver
28	chr15:78401000-78403800	Strong transcription	Thymus	Thymus
29	chr15:78401200-78402200	Strong transcription	Fetal Thymus	thymus
30	chr15:78401200-78403800	Strong transcription	Fetal Intestine Large	intestine
31	chr15:78401200-78405400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:78401200-78405400	Strong transcription	Fetal Intestine Small	intestine
33	chr15:78401400-78413000	Weak transcription	Fetal Stomach	stomach
34	chr15:78401400-78414400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:78401800-78402600	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:78402000-78403800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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