Variant report

Variant	rs335719
Chromosome Location	chr15:76234957-76234958
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76231213..76235489-chr15:76235646..76238510,7	K562	blood:
2	chr15:76228613..76230905-chr15:76232150..76235048,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169752	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1695372	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs1699275	0.93[AFR][1000 genomes]
rs2455893	1.00[YRI][hapmap]
rs2455895	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs2460810	0.91[AFR][1000 genomes]
rs2469037	0.88[YRI][hapmap];0.91[AFR][1000 genomes]
rs335689	1.00[YRI][hapmap]
rs335698	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs335707	1.00[YRI][hapmap]
rs335722	1.00[YRI][hapmap];0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1053717	chr15:76196674-76314542	Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1040053	chr15:76197988-76314542	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv904398	chr15:76220285-76359055	Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv569998	chr15:76232605-76550938	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs335719	GALNT14	trans	lymphoblastoid	seeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76211400-76240200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr15:76217200-76252000	Weak transcription	Pancreas	Pancrea
3	chr15:76223600-76236200	Weak transcription	Fetal Heart	heart
4	chr15:76226400-76236600	Weak transcription	Stomach Mucosa	stomach
5	chr15:76226600-76238600	Weak transcription	NHLF	lung
6	chr15:76226800-76235000	Weak transcription	Fetal Kidney	kidney
7	chr15:76227800-76236000	Weak transcription	Osteobl	bone
8	chr15:76228000-76235600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr15:76228000-76235600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:76228200-76239600	Weak transcription	Fetal Brain Female	brain
11	chr15:76228400-76236200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:76230400-76236000	Weak transcription	NHEK	skin
13	chr15:76230400-76236200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:76230400-76236600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:76230600-76236000	Weak transcription	HSMMtube	muscle
16	chr15:76230600-76238600	Weak transcription	Left Ventricle	heart
17	chr15:76230600-76239400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:76230600-76244400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:76230800-76238200	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr15:76230800-76246400	Weak transcription	Hela-S3	cervix
21	chr15:76231000-76239000	Weak transcription	Fetal Brain Male	brain
22	chr15:76231400-76239400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:76231600-76236000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr15:76231800-76236000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:76232200-76236000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:76232200-76238400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr15:76232200-76239400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:76232400-76235800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:76232400-76239200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:76232600-76236000	Weak transcription	HMEC	breast
31	chr15:76232800-76239400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:76233200-76236200	Weak transcription	NH-A	brain
33	chr15:76233400-76235600	Weak transcription	A549	lung
34	chr15:76233600-76235600	Weak transcription	HSMM	muscle
35	chr15:76234800-76235000	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links