Variant report

Variant	rs1236810
Chromosome Location	chr19:37966661-37966662
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	chr19:37959263..37961865-chr19:37965726..37969534,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196437	Chromatin interaction
ENSG00000171827	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1038085	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10403307	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10425671	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11883392	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1465434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1530500	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs1871197	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2045909	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2199644	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs256737	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs256739	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs2617789	1.00[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];0.96[TSI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972456	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2972459	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs45483504	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4803228	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62110388	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62110389	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62110390	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62110392	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62110395	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62110430	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62110431	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62110434	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6508729	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs6508738	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7251097	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs7254170	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs73027379	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73027386	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8108650	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8109709	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057688	chr19:37828019-37988253	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1056753	chr19:37963714-38015943	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1236810	IGFL4	cis	parietal	SCAN
rs1236810	EXOSC5	cis	cerebellum	SCAN
rs1236810	CATSPERG	cis	parietal	SCAN
rs1236810	ITPKC	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37961000-37966800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:37961000-37967800	Weak transcription	Pancreas	Pancrea
3	chr19:37961000-37973000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:37961000-37974000	Weak transcription	Stomach Mucosa	stomach
5	chr19:37961200-37967000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:37961400-37966800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:37961400-37967000	Weak transcription	Fetal Heart	heart
8	chr19:37961400-37970600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:37961400-37980400	ZNF genes & repeats	Liver	Liver
10	chr19:37961800-37967800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:37962200-37967800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr19:37962200-37968600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
13	chr19:37962200-37976200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:37962200-37976400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr19:37962200-37977800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr19:37962200-37977800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:37962400-37968600	Strong transcription	Placenta Amnion	Placenta Amnion
18	chr19:37962400-37977600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr19:37962400-37979200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:37962600-37966800	Weak transcription	HUVEC	blood vessel
21	chr19:37962800-37968600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
22	chr19:37963000-37970000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
23	chr19:37963200-37966800	Weak transcription	Brain Substantia Nigra	brain
24	chr19:37963200-37969400	ZNF genes & repeats	Fetal Brain Female	brain
25	chr19:37963200-37976600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
26	chr19:37963200-37981000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr19:37963800-37966800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr19:37963800-37969800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
29	chr19:37963800-37976400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
30	chr19:37963800-37985600	ZNF genes & repeats	Adipose Nuclei	Adipose
31	chr19:37964000-37968200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
32	chr19:37964000-37976400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
33	chr19:37964200-37977600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
34	chr19:37964400-37966800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:37964400-37968600	Strong transcription	Left Ventricle	heart
36	chr19:37964600-37966800	Weak transcription	NHDF-Ad	bronchial
37	chr19:37964800-37966800	Weak transcription	NH-A	brain
38	chr19:37964800-37968000	Strong transcription	Brain Hippocampus Middle	brain
39	chr19:37964800-37968600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:37965000-37966800	Weak transcription	HSMM	muscle
41	chr19:37965200-37966800	Weak transcription	Gastric	stomach
42	chr19:37965200-37968200	Strong transcription	Fetal Thymus	thymus
43	chr19:37965200-37968600	ZNF genes & repeats	Thymus	Thymus
44	chr19:37965200-37968800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:37965200-37969000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
46	chr19:37965400-37966800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr19:37965400-37966800	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr19:37965400-37968600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:37965400-37968600	ZNF genes & repeats	Fetal Intestine Large	intestine
50	chr19:37965400-37968600	Strong transcription	Fetal Stomach	stomach

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