Variant report

Variant	rs3762621
Chromosome Location	chr2:173306140-173306141
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173290118..173293854-chr2:173304445..173308429,5	MCF-7	breast:
2	chr2:173305651..173308111-chr2:173326516..173329013,2	MCF-7	breast:
3	chr2:173297263..173301573-chr2:173305902..173308346,3	MCF-7	breast:
4	chr2:173305610..173308515-chr2:173310023..173312671,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091409	Chromatin interaction
ENSG00000226963	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10497383	0.81[AMR][1000 genomes]
rs10497384	0.81[AMR][1000 genomes]
rs12469788	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17676243	0.81[AMR][1000 genomes]
rs17676773	0.81[AMR][1000 genomes]
rs17727678	0.81[AMR][1000 genomes]
rs17727732	0.81[AMR][1000 genomes]
rs2272498	0.81[AMR][1000 genomes]
rs36002642	0.83[AMR][1000 genomes]
rs3762620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792255	0.81[AMR][1000 genomes]
rs3792256	0.81[AMR][1000 genomes]
rs3828342	0.81[AMR][1000 genomes]
rs4972832	0.83[AMR][1000 genomes]
rs55726436	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433358	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6433359	0.81[AMR][1000 genomes]
rs6433360	0.81[AMR][1000 genomes]
rs6715294	0.83[AMR][1000 genomes]
rs6717877	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6718033	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6728123	0.83[AMR][1000 genomes]
rs6728419	0.81[AMR][1000 genomes]
rs6731691	0.81[AMR][1000 genomes]
rs6755605	0.81[AMR][1000 genomes]
rs7565670	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7594889	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
2	nsv875414	chr2:173267081-173307756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1847874	chr2:173277361-173308318	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv583663	chr2:173287832-173307756	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv583664	chr2:173289239-173307756	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173294800-173306400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:173294800-173308800	Enhancers	Stomach Mucosa	stomach
3	chr2:173295200-173306600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr2:173295200-173306600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr2:173295600-173308600	Enhancers	Fetal Intestine Large	intestine
6	chr2:173296000-173307600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr2:173296200-173307600	Enhancers	Fetal Thymus	thymus
8	chr2:173296600-173308600	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr2:173297000-173306600	Enhancers	Small Intestine	intestine
10	chr2:173297000-173307600	Enhancers	Pancreas	Pancrea
11	chr2:173297600-173307400	Enhancers	Spleen	Spleen
12	chr2:173300200-173307600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr2:173300400-173308000	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr2:173300600-173306600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:173301000-173308400	Enhancers	Fetal Intestine Small	intestine
16	chr2:173301200-173308400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:173301400-173308400	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr2:173302400-173307600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr2:173302400-173308200	Enhancers	HepG2	liver
20	chr2:173302600-173308000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr2:173303200-173307600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:173303200-173308400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:173303200-173309600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:173303400-173306400	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr2:173303600-173307600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:173303800-173306600	Enhancers	HSMMtube	muscle
27	chr2:173303800-173307600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:173304000-173306400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:173304000-173306400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:173304000-173306600	Weak transcription	Right Atrium	heart
31	chr2:173304200-173306400	Enhancers	NH-A	brain
32	chr2:173304200-173306600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:173304200-173306600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:173304200-173306800	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:173304200-173311400	Weak transcription	Liver	Liver
36	chr2:173304400-173306400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr2:173304400-173306600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:173304400-173306600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:173304600-173306400	Enhancers	Hela-S3	cervix
40	chr2:173304600-173306400	Enhancers	HMEC	breast
41	chr2:173304600-173306400	Weak transcription	Osteobl	bone
42	chr2:173304600-173306600	Weak transcription	NHDF-Ad	bronchial
43	chr2:173304600-173307000	Weak transcription	Brain Substantia Nigra	brain
44	chr2:173304600-173307600	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr2:173304600-173307600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:173304600-173307600	Enhancers	HUVEC	blood vessel
47	chr2:173304600-173308400	Enhancers	HSMM	muscle
48	chr2:173304600-173308800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:173304600-173310400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:173304800-173306400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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