Variant report

Variant	rs11730876
Chromosome Location	chr4:160147159-160147160
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	chr4:160144300..160148561-chr4:160148717..160151387,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109756	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11100211	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12502799	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12503790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12507531	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12508599	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12509160	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12509165	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13116575	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13119443	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13124646	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13152231	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56806866	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6536402	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67377365	0.87[EUR][1000 genomes]
rs7659528	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9992208	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016150	chr4:159995816-160165156	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830129	chr4:160061694-160270760	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	esv1795614	chr4:160142544-160161916	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11730876	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160102000-160149000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:160115600-160149200	Weak transcription	Esophagus	oesophagus
3	chr4:160116800-160148200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:160119000-160148600	Weak transcription	Small Intestine	intestine
5	chr4:160125200-160148600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr4:160127800-160148600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:160128000-160148600	Weak transcription	NHDF-Ad	bronchial
8	chr4:160128400-160148600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:160128600-160148400	Weak transcription	Stomach Mucosa	stomach
10	chr4:160129200-160148200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:160130800-160148600	Weak transcription	Ovary	ovary
12	chr4:160132400-160148600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:160132400-160148600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:160132400-160149200	Weak transcription	Brain Germinal Matrix	brain
15	chr4:160132800-160148000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:160133400-160171600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:160134200-160156600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:160138000-160156000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:160138800-160148600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr4:160141400-160148600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:160141400-160148800	Weak transcription	Fetal Muscle Leg	muscle
22	chr4:160141800-160148600	Weak transcription	Pancreas	Pancrea
23	chr4:160142600-160148600	Weak transcription	Gastric	stomach
24	chr4:160142600-160148600	Weak transcription	Left Ventricle	heart
25	chr4:160142600-160148800	Weak transcription	Psoas Muscle	Psoas
26	chr4:160143400-160148600	Weak transcription	Fetal Brain Female	brain
27	chr4:160143400-160148800	Weak transcription	Right Ventricle	heart
28	chr4:160143600-160148200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr4:160143600-160148400	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:160143600-160148600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr4:160143600-160148600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:160143600-160148600	Weak transcription	Right Atrium	heart
33	chr4:160143800-160148000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:160143800-160148600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:160143800-160148600	Weak transcription	Brain Substantia Nigra	brain
36	chr4:160143800-160148600	Weak transcription	Fetal Kidney	kidney
37	chr4:160143800-160148600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr4:160143800-160148600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:160144000-160148600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:160144000-160148600	Weak transcription	Brain Angular Gyrus	brain
41	chr4:160144000-160148600	Weak transcription	Brain Hippocampus Middle	brain
42	chr4:160144000-160148600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr4:160145800-160148600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:160145800-160148600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr4:160145800-160150400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr4:160146000-160148400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr4:160146000-160148600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr4:160146000-160148600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr4:160146000-160148600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr4:160146000-160148600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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