Variant report

Variant	rs1471431
Chromosome Location	chr19:39260194-39260195
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	chr19:39260117..39262134-chr19:39341376..39343069,2	K562	blood:
2	chr19:39260065..39260751-chr19:39420671..39421390,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104824	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000128626	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12972557	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12974327	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1471432	0.80[AFR][1000 genomes]
rs1966961	0.92[CEU][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1966962	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2279143	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs2368519	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2368521	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35620539	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4547457	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6508818	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7248248	0.96[EUR][1000 genomes]
rs7248831	0.90[EUR][1000 genomes]
rs7250933	0.93[EUR][1000 genomes]
rs7255028	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8100321	0.93[CEU][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8104072	0.89[EUR][1000 genomes]
rs8110500	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9304579	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9304580	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[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	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv1064688	chr19:39249059-39291526	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv1061904	chr19:39249692-39302843	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	nsv911670	chr19:39250308-39322087	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS 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	22 gene(s)	inside rSNPs	diseases
7	nsv911671	chr19:39252238-39306425	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
8	nsv911672	chr19:39252238-39318006	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1063592	chr19:39257977-39287265	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1471431	LGALS7B	cis	Esophagus Mucosa	GTEx
rs1471431	LGALS7	cis	Skin Sun Exposed Lower leg	GTEx
rs1471431	LGALS7B	cis	Skin Sun Exposed Lower leg	GTEx
rs1471431	LGALS7	cis	Esophagus Mucosa	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39246400-39270800	Weak transcription	K562	blood
2	chr19:39254200-39265400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:39255800-39260200	Weak transcription	Fetal Intestine Large	intestine
4	chr19:39256400-39260200	Weak transcription	A549	lung
5	chr19:39259400-39260200	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr19:39259800-39260200	Enhancers	Primary B cells from peripheral blood	blood
7	chr19:39259800-39260200	Enhancers	Primary hematopoietic stem cells	blood
8	chr19:39259800-39260200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr19:39259800-39260200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr19:39259800-39260200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:39259800-39260400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr19:39259800-39260600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:39259800-39261000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:39259800-39261000	Enhancers	Placenta Amnion	Placenta Amnion
15	chr19:39260000-39260200	Enhancers	H9 Cell Line	embryonic stem cell
16	chr19:39260000-39260200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr19:39260000-39260200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr19:39260000-39260200	Enhancers	Primary B cells from cord blood	blood
19	chr19:39260000-39260200	Enhancers	Primary T cells fromperipheralblood	blood
20	chr19:39260000-39260200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr19:39260000-39260200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:39260000-39260200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr19:39260000-39260200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr19:39260000-39260200	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr19:39260000-39260200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:39260000-39260200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:39260000-39260200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:39260000-39260200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:39260000-39260200	Enhancers	Colonic Mucosa	Colon
30	chr19:39260000-39260200	Enhancers	Fetal Intestine Small	intestine
31	chr19:39260000-39260200	Enhancers	Fetal Muscle Trunk	muscle
32	chr19:39260000-39260200	Enhancers	Fetal Muscle Leg	muscle
33	chr19:39260000-39260200	Enhancers	Fetal Thymus	thymus
34	chr19:39260000-39260200	Enhancers	Left Ventricle	heart
35	chr19:39260000-39260200	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr19:39260000-39260200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
37	chr19:39260000-39260200	Enhancers	Thymus	Thymus
38	chr19:39260000-39260200	Enhancers	HUVEC	blood vessel
39	chr19:39260000-39260200	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr19:39260000-39260400	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr19:39260000-39260400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:39260000-39260400	Enhancers	Esophagus	oesophagus
43	chr19:39260000-39260400	Flanking Active TSS	GM12878-XiMat	blood
44	chr19:39260000-39260400	Flanking Active TSS	NHEK	skin
45	chr19:39260000-39260600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:39260000-39261000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr19:39260000-39261000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:39260000-39261000	Enhancers	Lung	lung
49	chr19:39260000-39261000	Enhancers	Pancreas	Pancrea
50	chr19:39260000-39261000	Active TSS	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links