Variant report

Variant	rs3745964
Chromosome Location	chr19:38899548-38899549
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38894351..38897771-chr19:38897837..38899876,3	K562	blood:
2	chr19:38898700..38900861-chr19:38901125..38903986,3	K562	blood:
3	chr19:38897975..38900777-chr19:38905620..38907470,2	K562	blood:
4	chr1:12679613..12680441-chr19:38899277..38899779,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130244	Chromatin interaction
ENSG00000171777	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12462230	0.86[ASN][1000 genomes]
rs2072350	0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2074979	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2074980	0.84[ASN][1000 genomes]
rs2074981	1.00[GIH][hapmap];0.91[MEX][hapmap]
rs2286550	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2286551	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2302226	1.00[JPT][hapmap]
rs3745956	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3745960	0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3745961	0.86[ASN][1000 genomes]
rs3745962	0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3745963	1.00[CEU][hapmap]
rs4802399	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8112499	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	esv1803709	chr19:38874828-38900078	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv1055309	chr19:38896244-38945851	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3745964	SPINT2	cis	lymphoblastoid	seeQTL
rs3745964	FAM98C	cis	Liver	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38894400-38903400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:38894400-38908000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:38894600-38900400	Weak transcription	A549	lung
4	chr19:38894600-38900400	Weak transcription	NHDF-Ad	bronchial
5	chr19:38894600-38900400	Weak transcription	NHLF	lung
6	chr19:38894600-38900600	Weak transcription	NH-A	brain
7	chr19:38894600-38902000	Weak transcription	HSMM	muscle
8	chr19:38894600-38902000	Weak transcription	NHEK	skin
9	chr19:38894600-38907800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:38894600-38908000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr19:38894600-38908400	Weak transcription	Left Ventricle	heart
12	chr19:38894600-38908400	Weak transcription	HUVEC	blood vessel
13	chr19:38894800-38900000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr19:38894800-38900600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:38894800-38902400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:38894800-38908000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr19:38894800-38908400	Weak transcription	Small Intestine	intestine
18	chr19:38895000-38901000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:38895000-38901000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr19:38895000-38903400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:38895000-38905800	Weak transcription	Brain Germinal Matrix	brain
22	chr19:38895000-38907800	Weak transcription	GM12878-XiMat	blood
23	chr19:38895000-38908000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr19:38895000-38908400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr19:38895200-38900000	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr19:38895200-38904200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr19:38895200-38906200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr19:38895200-38907800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:38895200-38908200	Weak transcription	Fetal Thymus	thymus
30	chr19:38895400-38900000	Strong transcription	Fetal Intestine Small	intestine
31	chr19:38895400-38900000	Strong transcription	Fetal Stomach	stomach
32	chr19:38895400-38907800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr19:38895400-38908000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr19:38895600-38899600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:38895600-38899600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr19:38895600-38900000	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr19:38895600-38900600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr19:38895600-38906000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr19:38895800-38899800	Weak transcription	Fetal Brain Male	brain
40	chr19:38895800-38899800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr19:38895800-38900400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr19:38895800-38907600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr19:38896000-38900000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr19:38896400-38900800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr19:38896400-38902000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr19:38897400-38900400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr19:38897400-38900600	Weak transcription	HSMMtube	muscle
48	chr19:38897800-38900400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:38897800-38900600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:38897800-38907600	Weak transcription	Esophagus	oesophagus

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