Variant report

Variant	rs819269
Chromosome Location	chr4:56238263-56238264
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	chr4:56236823..56239564-chr4:56243563..56245351,2	MCF-7	breast:
2	chr4:56237917..56240536-chr4:56260724..56263321,2	K562	blood:

Variant related genes	Relation type
ENSG00000249700	Chromatin interaction
ENSG00000134851	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10010762	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10012559	0.84[CHB][hapmap]
rs10021233	1.00[CEU][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10024928	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1021307	0.81[TSI][hapmap]
rs10462028	0.87[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap]
rs1048004	0.81[TSI][hapmap]
rs11133375	0.89[CHB][hapmap]
rs17721497	0.81[TSI][hapmap]
rs17722979	0.81[TSI][hapmap]
rs17776975	0.81[TSI][hapmap]
rs1801260	0.81[TSI][hapmap]
rs1818460	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1961107	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1985606	0.88[CHB][hapmap]
rs2538	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28609134	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4089487	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41324951	0.81[TSI][hapmap]
rs475465	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs476184	1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs482114	0.82[AMR][1000 genomes]
rs483978	0.81[CHD][hapmap];0.95[GIH][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes]
rs496055	0.82[AMR][1000 genomes]
rs499110	0.82[AMR][1000 genomes]
rs525271	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs550144	0.81[TSI][hapmap]
rs552792	1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs552950	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs556072	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs572553	0.83[AMR][1000 genomes]
rs573960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs576732	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58506276	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62305200	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62305201	0.82[AMR][1000 genomes]
rs62305202	0.82[AMR][1000 genomes]
rs62306207	0.82[AMR][1000 genomes]
rs6554290	0.81[TSI][hapmap]
rs6851971	0.81[TSI][hapmap]
rs693367	0.81[CHD][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs7664100	0.89[CHB][hapmap]
rs819203	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs819266	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs819267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs819268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs819270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs861029	0.81[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap]
rs880358	0.81[TSI][hapmap]
rs9312660	0.80[EUR][1000 genomes]
rs9790808	0.88[CHB][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	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs819269	SRD5A2L	cis	multi-tissue	Pritchard
rs819269	TMEM165	cis	cerebellum	SCAN
rs819269	TMEM165	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56213600-56242600	Weak transcription	Gastric	stomach
2	chr4:56213800-56239000	Weak transcription	Brain Germinal Matrix	brain
3	chr4:56213800-56251400	Weak transcription	Pancreas	Pancrea
4	chr4:56214000-56241800	Weak transcription	Colonic Mucosa	Colon
5	chr4:56214400-56247600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:56219400-56238400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:56220800-56241400	Weak transcription	Primary T cells from cord blood	blood
8	chr4:56225800-56238400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:56225800-56244800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:56225800-56244800	Weak transcription	Stomach Mucosa	stomach
11	chr4:56226000-56238400	Weak transcription	Osteobl	bone
12	chr4:56226000-56238600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:56226000-56240400	Weak transcription	HSMM	muscle
14	chr4:56226000-56241200	Weak transcription	Esophagus	oesophagus
15	chr4:56226000-56245000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:56226000-56245000	Weak transcription	HSMMtube	muscle
17	chr4:56227800-56238400	Weak transcription	Placenta	Placenta
18	chr4:56228000-56244800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:56228400-56245400	Weak transcription	K562	blood
20	chr4:56228400-56251000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:56230400-56242000	Weak transcription	Ovary	ovary
22	chr4:56230600-56239200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr4:56230600-56239600	Weak transcription	Fetal Brain Female	brain
24	chr4:56230600-56240200	Weak transcription	Fetal Lung	lung
25	chr4:56230600-56241200	Weak transcription	Fetal Muscle Leg	muscle
26	chr4:56230600-56245200	Weak transcription	Fetal Intestine Small	intestine
27	chr4:56231800-56238400	Weak transcription	Thymus	Thymus
28	chr4:56232000-56241800	Weak transcription	Lung	lung
29	chr4:56232000-56247600	Weak transcription	Spleen	Spleen
30	chr4:56233200-56238400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:56233200-56241800	Weak transcription	Fetal Stomach	stomach
32	chr4:56233200-56261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr4:56233400-56239400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr4:56233800-56238600	Weak transcription	NH-A	brain
35	chr4:56234000-56244800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:56234200-56238400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr4:56234200-56238600	Weak transcription	Brain Anterior Caudate	brain
38	chr4:56234200-56238600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:56235800-56247600	Weak transcription	Aorta	Aorta
40	chr4:56236000-56240400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:56236400-56238600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:56236400-56240200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:56236400-56242200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr4:56236400-56248400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr4:56236600-56238400	Weak transcription	Brain Angular Gyrus	brain
46	chr4:56236600-56239800	Weak transcription	Fetal Thymus	thymus
47	chr4:56236800-56238400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:56236800-56239800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr4:56236800-56241600	Weak transcription	Dnd41	blood
50	chr4:56236800-56243800	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links