Variant report

Variant	rs3789088
Chromosome Location	chr2:111790804-111790805
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:111789979..111793920-chr2:111796275..111799559,5	MCF-7	breast:
2	chr2:111785222..111792269-chr2:111873385..111881089,20	MCF-7	breast:
3	chr2:111777002..111779950-chr2:111790531..111792084,2	MCF-7	breast:
4	chr2:111788554..111790871-chr2:111792372..111794007,2	MCF-7	breast:
5	chr2:111790430..111792678-chr2:111804599..111806279,2	MCF-7	breast:
6	chr2:111779153..111781716-chr2:111789597..111791988,2	MCF-7	breast:
7	chr2:111790298..111793489-chr2:111807175..111809652,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153094	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11123312	0.85[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.94[MKK][hapmap];0.86[ASN][1000 genomes]
rs11687123	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13012948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025923	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17041761	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1976055	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976056	0.80[EUR][1000 genomes]
rs35761487	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs35816855	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789076	0.85[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.94[MKK][hapmap];0.85[ASN][1000 genomes]
rs3789086	0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3789087	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789098	0.87[CEU][hapmap]
rs3789101	0.81[CEU][hapmap]
rs3827541	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs56068469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59554295	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72834597	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72836307	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7569167	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111786000-111795800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:111786200-111792400	Enhancers	Fetal Lung	lung
3	chr2:111786800-111792800	Enhancers	Fetal Intestine Small	intestine
4	chr2:111787000-111792000	Enhancers	Stomach Mucosa	stomach
5	chr2:111787000-111792800	Enhancers	Fetal Intestine Large	intestine
6	chr2:111787400-111795600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:111787800-111825400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:111788000-111791200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:111788000-111791600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:111788200-111791200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:111788200-111792600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:111788200-111793400	Weak transcription	Fetal Thymus	thymus
13	chr2:111788200-111799200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:111788600-111791400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:111789200-111791200	Enhancers	Left Ventricle	heart
16	chr2:111789200-111791200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr2:111789400-111791200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:111789600-111791200	Enhancers	Placenta	Placenta
19	chr2:111790000-111791400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr2:111790200-111791000	Enhancers	Placenta Amnion	Placenta Amnion
21	chr2:111790200-111791200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:111790200-111791200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:111790200-111791400	Enhancers	Primary B cells from cord blood	blood
24	chr2:111790200-111791400	Enhancers	NHEK	skin
25	chr2:111790200-111791600	Enhancers	HMEC	breast
26	chr2:111790200-111792400	Enhancers	Fetal Heart	heart
27	chr2:111790400-111791000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:111790400-111791200	Enhancers	Gastric	stomach
29	chr2:111790400-111791200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr2:111790800-111791000	Enhancers	Colonic Mucosa	Colon
31	chr2:111790800-111791000	Enhancers	Duodenum Mucosa	Duodenum
32	chr2:111790800-111791200	Enhancers	A549	lung
33	chr2:111790800-111791200	Enhancers	HepG2	liver
34	chr2:111790800-111791600	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr2:111790800-111793600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:111790800-111799200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:111790800-111800200	Weak transcription	Spleen	Spleen

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