Variant report

Variant	rs3789091
Chromosome Location	chr2:111788794-111788795
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	chr2:111785222..111792269-chr2:111873385..111881089,20	MCF-7	breast:
2	chr2:111788554..111790871-chr2:111792372..111794007,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153094	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10183208	0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10496436	0.92[CEU][hapmap]
rs11123295	0.82[ASN][1000 genomes]
rs11679060	0.82[ASN][1000 genomes]
rs11896172	0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1384792	0.82[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1483531	0.82[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs2062223	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2062224	0.92[CEU][hapmap]
rs2341657	0.82[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2341658	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs3761707	0.92[CEU][hapmap]
rs3789094	0.92[CEU][hapmap]
rs3789096	0.89[CEU][hapmap]
rs3827543	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4849327	0.82[JPT][hapmap]
rs4849341	0.82[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs6722565	0.92[CEU][hapmap]
rs6723578	0.92[CEU][hapmap]
rs6760171	0.84[CEU][hapmap]
rs7594735	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs7598867	0.92[CEU][hapmap]
rs7601853	0.92[CEU][hapmap]
rs967895	0.83[JPT][hapmap]

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	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv834330	chr2:111593290-111789447	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3789091	NCRNA00116	cis	cerebellum	SCAN
rs3789091	IL1F8	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111785600-111790200	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr2:111786000-111795800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr2:111786200-111792400	Enhancers	Fetal Lung	lung
4	chr2:111786400-111790400	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr2:111786600-111790600	Enhancers	Duodenum Mucosa	Duodenum
6	chr2:111786800-111790000	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr2:111786800-111792800	Enhancers	Fetal Intestine Small	intestine
8	chr2:111787000-111789000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr2:111787000-111789200	Enhancers	Fetal Heart	heart
10	chr2:111787000-111789800	Enhancers	Fetal Stomach	stomach
11	chr2:111787000-111792000	Enhancers	Stomach Mucosa	stomach
12	chr2:111787000-111792800	Enhancers	Fetal Intestine Large	intestine
13	chr2:111787400-111788800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:111787400-111789000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:111787400-111795600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:111787800-111790200	Bivalent Enhancer	HepG2	liver
17	chr2:111787800-111790200	Weak transcription	HMEC	breast
18	chr2:111787800-111825400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:111788000-111789600	Weak transcription	Small Intestine	intestine
20	chr2:111788000-111789600	Weak transcription	A549	lung
21	chr2:111788000-111789800	Weak transcription	Right Atrium	heart
22	chr2:111788000-111789800	Weak transcription	Spleen	Spleen
23	chr2:111788000-111790600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:111788000-111791200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:111788000-111791600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:111788200-111789200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:111788200-111789200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:111788200-111789600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:111788200-111789600	Weak transcription	Placenta	Placenta
30	chr2:111788200-111790200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:111788200-111790200	Weak transcription	Pancreas	Pancrea
32	chr2:111788200-111790600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:111788200-111791200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:111788200-111792600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:111788200-111793400	Weak transcription	Fetal Thymus	thymus
36	chr2:111788200-111799200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:111788400-111788800	Flanking Active TSS	GM12878-XiMat	blood
38	chr2:111788400-111789200	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr2:111788600-111789000	Weak transcription	Colonic Mucosa	Colon
40	chr2:111788600-111789800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:111788600-111790200	Weak transcription	Primary B cells from cord blood	blood
42	chr2:111788600-111791400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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