Variant report

Variant	rs2292719
Chromosome Location	chr3:120497835-120497836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:120491622..120494305-chr3:120496483..120498559,2	K562	blood:
2	chr3:120490765..120494305-chr3:120495076..120499796,4	K562	blood:
3	chr3:120495942..120499120-chr3:120500885..120503419,3	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10511404	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11714961	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12489104	0.85[TSI][hapmap];0.82[YRI][hapmap]
rs13316584	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1566988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs167722	0.86[ASN][1000 genomes]
rs172819	0.83[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs178725	0.87[ASN][1000 genomes]
rs2288096	0.81[TSI][hapmap];0.82[YRI][hapmap]
rs373188	0.87[ASN][1000 genomes]
rs417061	0.83[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs4501055	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs519336	0.83[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs55831173	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56406902	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs607953	0.83[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs618642	0.83[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs6778859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6796222	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73183726	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7430785	0.82[YRI][hapmap]
rs7620570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7633399	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9814744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9838458	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9854081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9872831	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9985346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv877378	chr3:120381530-120606438	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1005396	chr3:120460741-120580319	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv829700	chr3:120469191-120675763	Strong transcription Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1012541	chr3:120482402-120580319	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv1014477	chr3:120482402-120583166	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2292719	STXBP5L	cis	cerebellum	SCAN
rs2292719	FSTL1	cis	parietal	SCAN
rs2292719	ALDH1L1	cis	parietal	SCAN
rs2292719	SLC41A3	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120462800-120499800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:120462800-120500000	Weak transcription	Gastric	stomach
3	chr3:120462800-120503000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:120463000-120499800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:120463000-120502000	Weak transcription	Colonic Mucosa	Colon
6	chr3:120463000-120504200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:120463000-120504800	Weak transcription	Fetal Brain Male	brain
8	chr3:120463400-120503000	Weak transcription	Small Intestine	intestine
9	chr3:120470200-120499600	Weak transcription	HSMMtube	muscle
10	chr3:120470200-120499800	Weak transcription	Lung	lung
11	chr3:120482200-120505200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:120482200-120517600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:120483200-120509800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:120483400-120502000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:120483400-120521200	Weak transcription	Fetal Heart	heart
16	chr3:120485400-120499800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:120486000-120498800	Weak transcription	Stomach Mucosa	stomach
18	chr3:120486000-120505000	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:120486200-120501600	Strong transcription	Primary B cells from cord blood	blood
20	chr3:120486200-120502000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:120486400-120499800	Weak transcription	NHLF	lung
22	chr3:120486400-120502000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:120486600-120499200	Weak transcription	Ovary	ovary
24	chr3:120486600-120499800	Weak transcription	Fetal Stomach	stomach
25	chr3:120487200-120499200	Weak transcription	Left Ventricle	heart
26	chr3:120487200-120502000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:120487600-120503000	Weak transcription	Right Ventricle	heart
28	chr3:120487800-120501400	Weak transcription	Brain Angular Gyrus	brain
29	chr3:120488600-120503200	Weak transcription	Psoas Muscle	Psoas
30	chr3:120489000-120501600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:120489400-120502000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr3:120489600-120501600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:120489600-120502200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:120491600-120502000	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:120491600-120511000	Weak transcription	HMEC	breast
36	chr3:120491800-120499800	Weak transcription	Pancreas	Pancrea
37	chr3:120492000-120501600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:120492200-120498200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:120492200-120499200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:120492400-120510600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr3:120493200-120500000	Weak transcription	NHEK	skin
42	chr3:120493200-120501600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:120493400-120499400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:120493400-120501600	Strong transcription	Primary T cells from cord blood	blood
45	chr3:120493400-120501600	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr3:120493400-120503400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:120494400-120511000	Weak transcription	K562	blood
48	chr3:120495200-120503400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:120495400-120501400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:120495400-120510200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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