Variant report

Variant	rs11072728
Chromosome Location	chr15:78400673-78400674
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:78251353..78252448-chr15:78400281..78401311,8	MCF-7	breast:
2	chr15:78360788..78361560-chr15:78400133..78400927,2	MCF-7	breast:
3	chr15:78292050..78293044-chr15:78400416..78401371,3	K562	blood:
4	chr15:78400336..78401442-chr15:78532932..78533726,4	MCF-7	breast:
5	chr15:78293404..78294385-chr15:78400442..78401273,2	MCF-7	breast:
6	chr15:78291946..78293315-chr15:78400365..78401521,34	MCF-7	breast:
7	chr15:78292095..78293104-chr15:78399979..78401592,9	MCF-7	breast:
8	chr15:78258802..78259810-chr15:78400203..78401702,8	MCF-7	breast:
9	chr15:78367037..78369598-chr15:78400476..78402359,2	MCF-7	breast:
10	chr15:78194874..78195656-chr15:78400670..78401266,2	MCF-7	breast:
11	chr15:78394209..78398078-chr15:78398123..78400882,3	MCF-7	breast:
12	chr15:78369429..78370104-chr15:78400426..78400975,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBC1D2B-4	chr15:78400089-78400752	l_1195_chr15:78344341-78421177_testes

No data

Variant related genes	Relation type
ENSG00000167202	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10456	0.87[CEU][hapmap];0.84[LWK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11072727	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072729	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	0.84[ASN][1000 genomes]
rs12440984	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs16969507	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs16969508	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs16969514	0.93[CHB][hapmap];0.91[CHD][hapmap]
rs1971151	0.86[CHB][hapmap]
rs2304828	0.81[ASN][1000 genomes]
rs2304829	0.82[CEU][hapmap];0.91[ASN][1000 genomes]
rs2867922	0.93[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs3784328	0.86[CHB][hapmap]
rs59999498	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009267	0.84[ASN][1000 genomes]
rs62009270	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62009271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6495273	0.81[CEU][hapmap];0.87[ASN][1000 genomes]
rs7162025	0.87[ASN][1000 genomes]
rs7164338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72732564	0.84[ASN][1000 genomes]
rs7359294	0.86[CHB][hapmap]
rs8028859	0.87[ASN][1000 genomes]
rs8032449	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs8036417	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs9806257	0.84[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	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
rs11072728	PPCDC	cis	cerebellum	SCAN
rs11072728	CIB2	cis	multi-tissue	Pritchard
rs11072728	CIB2	cis	lymphoblastoid	seeQTL
rs11072728	CIB2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78393200-78406000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78393400-78401200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr15:78395000-78405600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:78395400-78405600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:78396000-78405400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:78396200-78405600	Weak transcription	Brain Anterior Caudate	brain
7	chr15:78396200-78421800	Weak transcription	Right Ventricle	heart
8	chr15:78396400-78404000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:78396400-78405400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr15:78396600-78405400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr15:78396600-78405600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:78396600-78423800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:78396800-78401400	Strong transcription	Fetal Stomach	stomach
14	chr15:78397000-78405600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:78397600-78401200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:78397600-78421400	Weak transcription	Fetal Muscle Leg	muscle
17	chr15:78398400-78405400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr15:78398400-78405600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:78398400-78423200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:78398600-78400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:78398600-78405200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:78398600-78405600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:78398600-78413200	Weak transcription	Spleen	Spleen
24	chr15:78398800-78400800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:78398800-78406200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:78399000-78402000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:78399000-78405400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr15:78399600-78401200	Enhancers	Placenta	Placenta
29	chr15:78399800-78400800	Enhancers	Primary T cells fromperipheralblood	blood
30	chr15:78400000-78400800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr15:78400000-78412800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:78400000-78422400	Weak transcription	Brain Germinal Matrix	brain
33	chr15:78400200-78414600	Weak transcription	Fetal Brain Female	brain
34	chr15:78400400-78400800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:78400600-78400800	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr15:78400600-78400800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr15:78400600-78400800	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr15:78400600-78400800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:78400600-78400800	Enhancers	Fetal Lung	lung
40	chr15:78400600-78400800	Enhancers	Pancreas	Pancrea
41	chr15:78400600-78400800	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr15:78400600-78400800	Enhancers	Right Atrium	heart
43	chr15:78400600-78400800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr15:78400600-78400800	Enhancers	GM12878-XiMat	blood
45	chr15:78400600-78400800	Enhancers	HepG2	liver
46	chr15:78400600-78400800	Enhancers	HSMMtube	muscle
47	chr15:78400600-78400800	Enhancers	NHLF	lung
48	chr15:78400600-78400800	Enhancers	Osteobl	bone
49	chr15:78400600-78401000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:78400600-78401000	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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