Variant report

Variant	rs2292804
Chromosome Location	chr4:16037084-16037085
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:16036340..16037856-chr4:16046034..16048272,2	MCF-7	breast:
2	chr4:16035503..16038004-chr4:16044490..16046008,2	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10939649	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11730129	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133886	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400771	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1850507	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2677795	0.86[CHB][hapmap]
rs884718	0.87[CHB][hapmap];0.86[CHD][hapmap];0.84[MEX][hapmap];0.82[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	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv916742	chr4:15797994-16064232	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2292804	PROM1	cis	Artery Aorta	GTEx
rs2292804	PROM1	cis	Artery Tibial	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16010800-16038600	Weak transcription	Placenta	Placenta
2	chr4:16025600-16045000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:16025600-16050600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:16025800-16057600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:16026400-16066600	Weak transcription	Colonic Mucosa	Colon
6	chr4:16026400-16066600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr4:16027200-16039000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:16030400-16039000	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr4:16031200-16040000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr4:16032800-16039800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:16033000-16037600	Enhancers	HepG2	liver
12	chr4:16033000-16039800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr4:16033200-16039200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr4:16033200-16039600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr4:16033800-16038400	Weak transcription	Primary B cells from cord blood	blood
16	chr4:16034400-16050400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:16034400-16072200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:16034800-16039000	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:16034800-16039800	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr4:16035000-16039000	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr4:16035000-16042800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:16035000-16044800	Weak transcription	Fetal Brain Female	brain
23	chr4:16035200-16050800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr4:16035200-16050800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:16035600-16040000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:16035800-16039200	Enhancers	H9 Cell Line	embryonic stem cell
27	chr4:16035800-16040000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:16036000-16037200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr4:16036000-16039600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr4:16036200-16037400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr4:16036200-16037400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr4:16036400-16037800	Strong transcription	Primary hematopoietic stem cells	blood
33	chr4:16036400-16037800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:16036400-16038000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr4:16036400-16038000	Weak transcription	Fetal Stomach	stomach
36	chr4:16036400-16039800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr4:16036400-16057800	Weak transcription	Fetal Intestine Small	intestine
38	chr4:16036600-16037200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:16036600-16038200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr4:16036600-16041600	Weak transcription	Fetal Heart	heart
41	chr4:16036600-16042000	Weak transcription	Fetal Brain Male	brain
42	chr4:16036600-16045200	Weak transcription	Pancreas	Pancrea
43	chr4:16036800-16037200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:16036800-16045200	Weak transcription	Stomach Mucosa	stomach
45	chr4:16037000-16038000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr4:16037000-16038200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr4:16037000-16038200	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr4:16037000-16039800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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