Variant report

Variant	rs3762619
Chromosome Location	chr2:173305885-173305886
allele	A/G
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	chr2:173305610..173308515-chr2:173310023..173312671,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091409	Chromatin interaction
ENSG00000226963	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10171775	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10175670	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10184567	0.87[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10195932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10197251	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10497381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10497385	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1076595	0.91[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs12465295	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs12465442	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs12467358	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs12469875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12469958	0.92[EUR][1000 genomes]
rs12473999	0.81[ASN][1000 genomes]
rs12477247	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs12477594	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12478465	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12622044	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1574247	0.86[EUR][1000 genomes]
rs16860377	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16860543	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2293646	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs2357415	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs28464102	0.81[ASN][1000 genomes]
rs28540552	0.86[ASN][1000 genomes]
rs3792257	0.92[EUR][1000 genomes]
rs3792260	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs3934627	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4281870	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4480959	0.96[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4993282	0.87[ASN][1000 genomes]
rs4993283	0.87[ASN][1000 genomes]
rs56084828	0.92[EUR][1000 genomes]
rs60275829	0.90[EUR][1000 genomes]
rs6718477	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs6721597	0.86[ASN][1000 genomes]
rs6755100	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs7567159	0.87[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs7604441	0.83[CHB][hapmap];0.84[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	chr2:173303800-173306000	Weak transcription	Placenta	Placenta
27	chr2:173303800-173306600	Enhancers	HSMMtube	muscle
28	chr2:173303800-173307600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:173304000-173306000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:173304000-173306000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:173304000-173306400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:173304000-173306400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:173304000-173306600	Weak transcription	Right Atrium	heart
34	chr2:173304200-173306400	Enhancers	NH-A	brain
35	chr2:173304200-173306600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:173304200-173306600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:173304200-173306800	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:173304200-173311400	Weak transcription	Liver	Liver
39	chr2:173304400-173306400	Enhancers	Muscle Satellite Cultured Cells	--
40	chr2:173304400-173306600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:173304400-173306600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:173304600-173306000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr2:173304600-173306400	Enhancers	Hela-S3	cervix
44	chr2:173304600-173306400	Enhancers	HMEC	breast
45	chr2:173304600-173306400	Weak transcription	Osteobl	bone
46	chr2:173304600-173306600	Weak transcription	NHDF-Ad	bronchial
47	chr2:173304600-173307000	Weak transcription	Brain Substantia Nigra	brain
48	chr2:173304600-173307600	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr2:173304600-173307600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:173304600-173307600	Enhancers	HUVEC	blood vessel

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