Variant report

Variant	rs4669751
Chromosome Location	chr2:11706693-11706694
allele	C/T
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	chr2:11706620-11707545	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:11703337-11709175	MCF-7	breast:	n/a	n/a
3	POLR2A	chr2:11706476-11706868	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:11706613-11707188	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RNA5SP85	TF binding region

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs13429194	0.94[ASN][1000 genomes]
rs4313952	0.94[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs6432210	0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs6432211	0.94[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs6432212	0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs6432213	0.94[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs6432214	0.82[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs6432215	0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs6432216	1.00[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.90[ASN][1000 genomes]
rs6432218	0.86[JPT][hapmap]
rs6432219	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6740248	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6749404	0.94[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs7565567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs930310	0.94[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.86[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	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
4	esv1814335	chr2:11689048-11718858	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4669751	GREB1	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11690000-11711000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:11694800-11755200	Weak transcription	Gastric	stomach
4	chr2:11697000-11706800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:11697000-11710800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:11697000-11722600	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:11697000-11723000	Weak transcription	Brain Anterior Caudate	brain
8	chr2:11697000-11723200	Weak transcription	Brain Angular Gyrus	brain
9	chr2:11697800-11706800	Weak transcription	Brain Substantia Nigra	brain
10	chr2:11698600-11713200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:11698600-11713400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:11698800-11713400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:11699000-11714400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:11699400-11706800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:11699800-11708400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:11699800-11713200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:11699800-11718400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:11699800-11723000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:11700000-11767000	Weak transcription	Right Atrium	heart
20	chr2:11700200-11712400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:11700200-11713800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:11700200-11723000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:11700400-11706800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:11700400-11713000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:11700400-11718400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:11700600-11709600	Genic enhancers	Ovary	ovary
27	chr2:11701800-11709400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:11702000-11711000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:11702800-11709400	Weak transcription	Pancreas	Pancrea
30	chr2:11702800-11720200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:11702800-11722400	Strong transcription	HepG2	liver
32	chr2:11703000-11713400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:11703000-11717400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:11704000-11720600	Weak transcription	Fetal Heart	heart
35	chr2:11705200-11707000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:11705200-11713600	Weak transcription	Fetal Lung	lung
37	chr2:11705600-11714600	Weak transcription	Psoas Muscle	Psoas
38	chr2:11706000-11712800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr2:11706200-11708000	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:11706400-11706800	Enhancers	K562	blood
41	chr2:11706600-11707000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:11706600-11707800	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr2:11706600-11708200	Strong transcription	Fetal Stomach	stomach
44	chr2:11706600-11708800	Strong transcription	Fetal Muscle Trunk	muscle

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