Variant report

Variant	rs13394619
Chromosome Location	chr2:11727507-11727508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:11726444-11727979	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:11727467-11727726	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:11712005-11732311	MCF-7	breast:	n/a	n/a
4	PML	chr2:11727478-11728186	MCF-7	breast:	n/a	n/a
5	POLR2A	chr2:11725017-11728081	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
GREB1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10165819	0.88[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10200851	0.91[ASW][hapmap];0.88[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10929759	0.85[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs11674605	0.92[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11679686	0.91[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12468019	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12470971	0.83[CHD][hapmap]
rs12473442	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12993278	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13016186	0.93[EUR][1000 genomes]
rs13017593	0.94[EUR][1000 genomes]
rs1529868	0.81[JPT][hapmap]
rs2358040	0.91[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2884374	0.91[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4669752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6746291	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7576826	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9287734	0.92[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9678410	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9789414	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9798272	0.90[AMR][1000 genomes];0.97[EUR][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	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
3	nsv873663	chr2:11664349-11783775	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Endometriosis	23104006	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13394619	GREB1	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11694800-11755200	Weak transcription	Gastric	stomach
3	chr2:11700000-11767000	Weak transcription	Right Atrium	heart
4	chr2:11711600-11738600	Weak transcription	Left Ventricle	heart
5	chr2:11714400-11765000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:11717600-11767000	Weak transcription	Fetal Intestine Small	intestine
7	chr2:11719200-11738000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:11719400-11750800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:11720000-11735600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:11721600-11733000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:11723000-11740400	Weak transcription	Liver	Liver
12	chr2:11723200-11735400	Weak transcription	Brain Substantia Nigra	brain
13	chr2:11723400-11735200	Weak transcription	Fetal Lung	lung
14	chr2:11723400-11740000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:11723600-11735200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:11723600-11735600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:11723600-11738600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:11724200-11732800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:11724200-11732800	Weak transcription	Pancreas	Pancrea
20	chr2:11724400-11735200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:11724400-11735200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr2:11724400-11738000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:11724400-11738600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:11724400-11788600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:11724600-11732800	Strong transcription	HepG2	liver
26	chr2:11724600-11735400	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:11724600-11741000	Weak transcription	Brain Anterior Caudate	brain
28	chr2:11724600-11766800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:11724600-11766800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:11724800-11735400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:11724800-11735600	Weak transcription	Brain Angular Gyrus	brain
32	chr2:11724800-11736000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:11724800-11749600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:11725000-11743800	Weak transcription	Fetal Kidney	kidney
35	chr2:11725200-11730200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:11725200-11730600	Strong transcription	Fetal Muscle Trunk	muscle
37	chr2:11725400-11728200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:11725400-11742400	Strong transcription	Ovary	ovary
39	chr2:11725600-11766800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:11725800-11727600	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr2:11725800-11728600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:11725800-11729400	Strong transcription	Fetal Muscle Leg	muscle
43	chr2:11725800-11730800	Strong transcription	Fetal Stomach	stomach
44	chr2:11726600-11728400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:11726600-11735400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:11727200-11727600	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:11727200-11733000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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