Variant report

Variant	rs1535470
Chromosome Location	chr13:50260029-50260030
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50258462..50260266-chr13:50263653..50266586,2	MCF-7	breast:
2	chr13:50254223..50257561-chr13:50258855..50261948,4	K562	blood:
3	chr13:50258208..50260676-chr13:50262902..50265227,2	K562	blood:

Variant related genes	Relation type
ENSG00000123179	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12858548	0.83[EUR][1000 genomes]
rs12859620	0.85[EUR][1000 genomes]
rs13313256	0.90[JPT][hapmap]
rs1535544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3903768	0.90[JPT][hapmap]
rs6561551	0.81[CEU][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs737250	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs7999786	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs942031	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs9535292	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs9568304	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs9591296	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv541772	chr13:50218255-50264414	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1535470	EBPL	cis	Whole Blood	GTEx
rs1535470	EBPL	cis	multi-tissue	Pritchard
rs1535470	EBPL	cis	Esophagus Mucosa	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50241000-50264800	Weak transcription	Aorta	Aorta
2	chr13:50242200-50260600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr13:50242200-50261000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr13:50242200-50261400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr13:50242200-50264200	Weak transcription	K562	blood
6	chr13:50242200-50264400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr13:50242200-50264400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr13:50242400-50260200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr13:50242400-50260400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr13:50242400-50261400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr13:50242400-50261400	Weak transcription	Gastric	stomach
12	chr13:50242400-50262200	Weak transcription	Spleen	Spleen
13	chr13:50242400-50263200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr13:50242400-50263800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr13:50242400-50264000	Weak transcription	Thymus	Thymus
16	chr13:50242400-50264400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr13:50242400-50264400	Weak transcription	Adipose Nuclei	Adipose
18	chr13:50242400-50264400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr13:50244400-50264400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr13:50245800-50261400	Weak transcription	HUVEC	blood vessel
21	chr13:50246000-50264600	Weak transcription	Left Ventricle	heart
22	chr13:50246200-50261400	Weak transcription	Hela-S3	cervix
23	chr13:50247000-50264400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr13:50248400-50263600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr13:50249400-50263600	Weak transcription	Primary B cells from cord blood	blood
26	chr13:50250400-50264400	Weak transcription	Primary T cells from cord blood	blood
27	chr13:50251400-50264400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr13:50251600-50264400	Weak transcription	HSMMtube	muscle
29	chr13:50251800-50262200	Weak transcription	Pancreas	Pancrea
30	chr13:50251800-50263600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr13:50253600-50264800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr13:50253800-50261400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr13:50253800-50264000	Weak transcription	Ovary	ovary
34	chr13:50253800-50264400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr13:50253800-50264400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr13:50254000-50260200	Weak transcription	Fetal Thymus	thymus
37	chr13:50254000-50264400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr13:50254400-50261200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr13:50254400-50264400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr13:50254400-50264400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr13:50254400-50264400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr13:50254400-50264600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr13:50254400-50264600	Weak transcription	Esophagus	oesophagus
44	chr13:50254600-50261200	Weak transcription	A549	lung
45	chr13:50254600-50261400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr13:50254600-50264200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr13:50255200-50264400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr13:50255400-50261400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr13:50256000-50262000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr13:50256200-50264600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links