Variant report

Variant	rs1675496
Chromosome Location	chr3:159583518-159583519
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	chr3:159575817..159579356-chr3:159581555..159584258,3	MCF-7	breast:
2	chr17:57925518..57927077-chr3:159581643..159584059,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1009058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936179	0.83[CEU][hapmap]
rs1497762	0.89[CEU][hapmap];0.83[GIH][hapmap]
rs1553081	0.89[CEU][hapmap]
rs16847223	0.80[MEX][hapmap]
rs2010748	0.89[CEU][hapmap]
rs33051	0.83[MEX][hapmap]
rs33053	0.84[CEU][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs33055	0.96[MEX][hapmap]
rs3889310	0.89[CEU][hapmap]
rs4679863	0.89[CEU][hapmap];0.83[GIH][hapmap];0.80[TSI][hapmap]
rs4679865	0.89[CEU][hapmap]
rs4680521	0.89[CEU][hapmap]
rs62270404	0.96[ASN][1000 genomes]
rs6780187	0.89[CEU][hapmap]
rs7639937	0.89[CEU][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	nsv877698	chr3:159583518-159640152	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159572400-159589400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:159574800-159584800	Enhancers	Brain Angular Gyrus	brain
3	chr3:159574800-159586200	Weak transcription	Ovary	ovary
4	chr3:159576800-159584200	Enhancers	Fetal Heart	heart
5	chr3:159577800-159584800	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr3:159578200-159585600	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr3:159578600-159585200	Weak transcription	Fetal Intestine Large	intestine
8	chr3:159579200-159584200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:159579400-159584200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:159579400-159587400	Weak transcription	Fetal Intestine Small	intestine
11	chr3:159579400-159589600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:159579400-159589600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:159579600-159584800	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr3:159579600-159589200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:159579600-159589600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:159579600-159589600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:159579600-159599200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:159579600-159600600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:159579800-159585200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:159579800-159588600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:159580000-159590200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:159580200-159584800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:159580200-159585600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:159580200-159587800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:159580200-159589400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:159580200-159589400	Weak transcription	NHEK	skin
27	chr3:159580200-159597600	Weak transcription	Spleen	Spleen
28	chr3:159580400-159584800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:159580400-159585200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:159580400-159586200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:159581400-159584600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr3:159581400-159585000	Enhancers	Brain Substantia Nigra	brain
33	chr3:159581600-159584200	Enhancers	Brain Anterior Caudate	brain
34	chr3:159581600-159584600	Enhancers	Rectal Smooth Muscle	rectum
35	chr3:159581600-159584800	Enhancers	Colon Smooth Muscle	Colon
36	chr3:159581600-159585200	Enhancers	Brain Cingulate Gyrus	brain
37	chr3:159581800-159584200	Enhancers	Fetal Kidney	kidney
38	chr3:159581800-159584400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:159581800-159584400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:159581800-159584800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:159581800-159585600	Enhancers	NHLF	lung
42	chr3:159582000-159584200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:159582200-159584000	Enhancers	Fetal Muscle Leg	muscle
44	chr3:159582400-159583600	Enhancers	Aorta	Aorta
45	chr3:159582400-159584400	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr3:159582400-159584800	Enhancers	HSMM	muscle
47	chr3:159582400-159584800	Enhancers	HSMMtube	muscle
48	chr3:159582600-159583600	Enhancers	Right Atrium	heart
49	chr3:159582600-159583800	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr3:159582600-159583800	Weak transcription	Fetal Brain Male	brain

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