Variant report

Variant	rs1025497
Chromosome Location	chr19:41871254-41871255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr19:41869070-41871296	A549	lung:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41858281..41860213-chr19:41869974..41872050,2	MCF-7	breast:
2	chr19:41856910..41863042-chr19:41867113..41873191,18	MCF-7	breast:
3	chr19:41870450..41872597-chr19:41951300..41953868,2	K562	blood:
4	chr19:41858489..41863412-chr19:41867730..41871601,11	K562	blood:
5	chr19:41868161..41871707-chr19:41902716..41905358,4	MCF-7	breast:
6	chr19:41869689..41871301-chr19:41934522..41938582,3	MCF-7	breast:
7	chr19:41868336..41871272-chr19:41944233..41948538,5	K562	blood:
8	chr19:41824554..41827469-chr19:41868894..41871689,2	K562	blood:
9	chr19:41868160..41871597-chr19:41899998..41904284,10	K562	blood:
10	chr19:41869853..41871782-chr19:41881681..41884054,2	K562	blood:
11	chr19:41814494..41816860-chr19:41868645..41871305,2	K562	blood:
12	chr19:41816143..41817649-chr19:41870161..41871689,2	MCF-7	breast:

No data

Variant related genes	Relation type
B9D2	TF binding region
ENSG00000255730	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000105341	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000142039	Chromatin interaction
ENSG00000268987	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000177191	Chromatin interaction
ENSG00000077348	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1046909	0.88[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11083616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083617	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11666933	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11670143	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11670739	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12462166	0.95[ASN][1000 genomes]
rs12983775	0.91[ASN][1000 genomes]
rs1549933	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1800469	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1800470	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1963413	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1982072	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2241712	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2241713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2241715	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2317130	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34503210	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4803457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803458	0.89[ASN][1000 genomes]
rs4803459	0.89[ASN][1000 genomes]
rs7260340	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8108357	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9797885	0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521311	chr19:41856886-41882712	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1025497	CTC-435M10.6	cis	Whole Blood	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41870200-41871400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr19:41870200-41871800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr19:41870400-41871400	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr19:41870600-41882000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr19:41870800-41871400	Enhancers	Primary hematopoietic stem cells	blood
6	chr19:41870800-41874000	Weak transcription	Esophagus	oesophagus
7	chr19:41870800-41874000	Weak transcription	Small Intestine	intestine
8	chr19:41870800-41882000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:41871000-41871400	Enhancers	Liver	Liver
10	chr19:41871000-41871600	Enhancers	HepG2	liver
11	chr19:41871000-41872200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:41871000-41872200	Weak transcription	Hela-S3	cervix
13	chr19:41871000-41872400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr19:41871000-41872400	Genic enhancers	Fetal Intestine Small	intestine
15	chr19:41871000-41872400	Enhancers	Fetal Muscle Leg	muscle
16	chr19:41871000-41872400	Weak transcription	Placenta	Placenta
17	chr19:41871000-41872600	Enhancers	Fetal Thymus	thymus
18	chr19:41871000-41872800	Weak transcription	HMEC	breast
19	chr19:41871000-41872800	Weak transcription	NHLF	lung
20	chr19:41871000-41873000	Weak transcription	Osteobl	bone
21	chr19:41871000-41873400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:41871000-41873400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr19:41871000-41873600	Weak transcription	Stomach Mucosa	stomach
24	chr19:41871000-41873600	Weak transcription	HSMM	muscle
25	chr19:41871000-41873600	Weak transcription	NH-A	brain
26	chr19:41871000-41873800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr19:41871000-41874000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr19:41871000-41876600	Weak transcription	Fetal Kidney	kidney
29	chr19:41871000-41879800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:41871000-41879800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr19:41871000-41880000	Weak transcription	HSMMtube	muscle
32	chr19:41871000-41881800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr19:41871000-41882000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr19:41871000-41882000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:41871000-41882000	Weak transcription	Primary T cells from cord blood	blood
36	chr19:41871200-41871400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:41871200-41871400	Enhancers	Placenta Amnion	Placenta Amnion
38	chr19:41871200-41871400	Enhancers	Dnd41	blood
39	chr19:41871200-41871400	Enhancers	K562	blood
40	chr19:41871200-41871600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr19:41871200-41871600	Enhancers	Adipose Nuclei	Adipose
42	chr19:41871200-41871600	Enhancers	A549	lung
43	chr19:41871200-41872200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:41871200-41872200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:41871200-41872200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:41871200-41872200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:41871200-41872200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:41871200-41872200	Weak transcription	Fetal Intestine Large	intestine
49	chr19:41871200-41872200	Weak transcription	Fetal Stomach	stomach
50	chr19:41871200-41872200	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links