Variant report

Variant	rs3769289
Chromosome Location	chr2:173727773-173727774
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	chr2:173723159..173726097-chr2:173727681..173729717,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091428	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12471745	1.00[YRI][hapmap]
rs12474304	1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap]
rs12478288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12612612	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[EUR][1000 genomes]
rs12618968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12622141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16823271	1.00[YRI][hapmap]
rs17706463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17754879	1.00[ASW][hapmap]
rs3769295	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3769314	1.00[YRI][hapmap]
rs3820852	1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173723400-173728800	Weak transcription	Pancreas	Pancrea
2	chr2:173724200-173727800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr2:173724400-173727800	Enhancers	Fetal Stomach	stomach
4	chr2:173724800-173727800	Enhancers	Fetal Lung	lung
5	chr2:173725000-173728000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:173725200-173728000	Weak transcription	Fetal Intestine Large	intestine
7	chr2:173725600-173727800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr2:173725800-173727800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:173725800-173728600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:173726000-173727800	Enhancers	Brain Anterior Caudate	brain
11	chr2:173726000-173734400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:173726200-173727800	Enhancers	Right Atrium	heart
13	chr2:173726200-173734400	Weak transcription	NHEK	skin
14	chr2:173726200-173734600	Weak transcription	HUVEC	blood vessel
15	chr2:173726600-173727800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:173726600-173727800	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr2:173726800-173729000	Weak transcription	Gastric	stomach
18	chr2:173726800-173729000	Weak transcription	Left Ventricle	heart
19	chr2:173726800-173753600	Weak transcription	Brain Angular Gyrus	brain
20	chr2:173727000-173727800	Enhancers	Small Intestine	intestine
21	chr2:173727400-173728200	Enhancers	Adipose Nuclei	Adipose
22	chr2:173727400-173729000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:173727600-173727800	Enhancers	Brain Hippocampus Middle	brain
24	chr2:173727600-173728400	Enhancers	Duodenum Mucosa	Duodenum

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