Variant report

Variant	rs1888150
Chromosome Location	chr9:13262789-13262790
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	chr9:13261386..13263235-chr9:13277146..13279520,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000107186	Chromatin interaction
ENSG00000234740	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10738329	0.89[GIH][hapmap]
rs10809923	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10809926	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790299	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13283251	0.81[CEU][hapmap]
rs13290727	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13297131	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13297480	0.84[GIH][hapmap]
rs1330134	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1412112	0.89[GIH][hapmap]
rs16930206	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1854665	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980994	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2149988	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34101279	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34423860	1.00[ASN][1000 genomes]
rs34504254	1.00[ASN][1000 genomes]
rs34714632	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34862901	1.00[ASN][1000 genomes]
rs4392997	1.00[ASN][1000 genomes]
rs7029241	0.89[GIH][hapmap]
rs7047995	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71507372	1.00[ASN][1000 genomes]
rs7866658	0.92[MKK][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892578	chr9:12942956-13485035	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv892583	chr9:13166139-13350478	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv892584	chr9:13214871-13350478	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv427838	chr9:13229753-13393890	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1888150	MPDZ	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13189000-13268600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:13208200-13265000	Weak transcription	Aorta	Aorta
3	chr9:13209800-13266000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr9:13219800-13265600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:13224000-13264600	Weak transcription	Osteobl	bone
6	chr9:13226800-13278000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr9:13232400-13264800	Weak transcription	NH-A	brain
8	chr9:13236400-13264400	Weak transcription	Fetal Intestine Small	intestine
9	chr9:13238000-13264800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr9:13240000-13278000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:13240800-13263000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:13243000-13264800	Weak transcription	Ovary	ovary
13	chr9:13244200-13267600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:13245800-13264800	Weak transcription	A549	lung
15	chr9:13247800-13266000	Weak transcription	HSMM	muscle
16	chr9:13248000-13264800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr9:13248000-13267800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr9:13248000-13268600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:13248800-13265000	Weak transcription	Fetal Stomach	stomach
20	chr9:13251600-13265200	Weak transcription	Right Atrium	heart
21	chr9:13252200-13267600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr9:13252800-13265000	Weak transcription	Left Ventricle	heart
23	chr9:13254000-13265200	Weak transcription	Brain Angular Gyrus	brain
24	chr9:13255000-13277200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:13255600-13265200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:13256000-13267600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:13256200-13264600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:13256400-13265000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:13256600-13265400	Weak transcription	Brain Anterior Caudate	brain
30	chr9:13256600-13266800	Weak transcription	Brain Germinal Matrix	brain
31	chr9:13256600-13269800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr9:13256800-13277600	Weak transcription	Fetal Muscle Leg	muscle
33	chr9:13257200-13267200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr9:13258600-13266200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr9:13258800-13265200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:13259600-13263200	Weak transcription	HUVEC	blood vessel
37	chr9:13259600-13265200	Weak transcription	Right Ventricle	heart
38	chr9:13261800-13265000	Weak transcription	Psoas Muscle	Psoas
39	chr9:13262000-13263000	Weak transcription	Colon Smooth Muscle	Colon
40	chr9:13262000-13264800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:13262000-13266200	Weak transcription	Fetal Lung	lung
42	chr9:13262200-13264400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr9:13262600-13264600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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