Variant report

Variant	rs1006412
Chromosome Location	chr13:76218076-76218077
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:76215940..76218613-chr13:76237848..76240059,2	K562	blood:
2	chr13:76111172..76113828-chr13:76216732..76219356,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188243	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs17704212	0.87[EUR][1000 genomes]
rs1951831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2093751	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34444653	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7317170	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73225909	0.87[EUR][1000 genomes]
rs735821	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7988966	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9565179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9573596	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9573597	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9573601	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751152	chr13:76144199-76288418	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv949152	chr13:76211453-76366622	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1006412	RP11-173B14.5	cis	lung	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76211400-76226200	Weak transcription	Left Ventricle	heart
2	chr13:76211600-76232800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr13:76211600-76235600	Weak transcription	Ovary	ovary
4	chr13:76211600-76235600	Weak transcription	Pancreas	Pancrea
5	chr13:76211800-76218800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr13:76211800-76230000	Weak transcription	Thymus	Thymus
7	chr13:76212000-76223200	Weak transcription	Fetal Stomach	stomach
8	chr13:76212200-76235600	Weak transcription	Aorta	Aorta
9	chr13:76212400-76230000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr13:76212400-76240400	Weak transcription	HMEC	breast
11	chr13:76212600-76222800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr13:76212800-76224600	Weak transcription	Fetal Kidney	kidney
13	chr13:76213000-76221600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr13:76213400-76267800	Weak transcription	Primary T cells from cord blood	blood
15	chr13:76213800-76235600	Weak transcription	Psoas Muscle	Psoas
16	chr13:76215400-76218400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr13:76215400-76258200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr13:76215600-76219800	Weak transcription	HSMMtube	muscle
19	chr13:76215600-76220000	Weak transcription	GM12878-XiMat	blood
20	chr13:76215600-76223600	Genic enhancers	Muscle Satellite Cultured Cells	--
21	chr13:76216200-76229400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr13:76217000-76218200	Transcr. at gene 5' and 3'	Osteobl	bone
23	chr13:76217000-76220000	Genic enhancers	NHDF-Ad	bronchial
24	chr13:76217200-76218200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr13:76217200-76218200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr13:76217200-76219000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr13:76217200-76222000	Genic enhancers	HSMM	muscle
28	chr13:76217400-76218600	Weak transcription	NH-A	brain
29	chr13:76217400-76223800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr13:76217600-76218200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr13:76217600-76218800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr13:76217600-76219800	Weak transcription	NHLF	lung
33	chr13:76217800-76218200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links