Variant report

Variant	rs1024271
Chromosome Location	chr13:52117313-52117314
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52114829..52118630-chr13:52158674..52160777,3	MCF-7	breast:
2	chr13:52097892..52100856-chr13:52116371..52118761,2	MCF-7	breast:
3	chr13:52024743..52028940-chr13:52112359..52118516,11	MCF-7	breast:
4	chr13:52025591..52028718-chr13:52111998..52119680,9	MCF-7	breast:
5	chr13:52025248..52027565-chr13:52113097..52117557,5	K562	blood:

Variant related genes	Relation type
ENSG00000224892	Chromatin interaction
ENSG00000206920	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000102786	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12585249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17075902	0.95[JPT][hapmap]
rs17532412	1.00[YRI][hapmap]
rs3803201	0.95[JPT][hapmap]
rs3825410	0.95[JPT][hapmap]
rs4075628	0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4625625	0.95[JPT][hapmap]
rs4941703	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4943005	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs745374	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9316547	0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9316548	0.85[ASN][1000 genomes]
rs9535744	1.00[YRI][hapmap]
rs9563061	1.00[CEU][hapmap]
rs9563063	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9563065	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9563066	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9563067	0.95[JPT][hapmap]
rs9568621	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9568633	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568644	0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes]
rs9568650	0.95[JPT][hapmap]
rs9805172	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[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	esv1797261	chr13:52100949-52139113	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52113000-52117600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr13:52113200-52117400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr13:52114400-52122800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr13:52114600-52117400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr13:52114800-52117400	Enhancers	Duodenum Smooth Muscle	Duodenum
6	chr13:52115200-52117800	Enhancers	Fetal Stomach	stomach
7	chr13:52115800-52117400	Enhancers	Fetal Lung	lung
8	chr13:52116000-52117400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr13:52116000-52117600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr13:52116000-52117600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr13:52116000-52117800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr13:52116200-52117400	Enhancers	Brain Substantia Nigra	brain
13	chr13:52116600-52117400	Active TSS	A549	lung
14	chr13:52116800-52117400	Enhancers	Fetal Kidney	kidney
15	chr13:52116800-52123000	Weak transcription	Hela-S3	cervix
16	chr13:52116800-52132000	Weak transcription	Pancreas	Pancrea
17	chr13:52117000-52117400	Enhancers	Colon Smooth Muscle	Colon
18	chr13:52117000-52117400	Active TSS	Ovary	ovary
19	chr13:52117000-52117600	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr13:52117000-52126200	Weak transcription	Adipose Nuclei	Adipose
21	chr13:52117200-52117400	Enhancers	HepG2	liver
22	chr13:52117200-52122600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr13:52117200-52122800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr13:52117200-52122800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr13:52117200-52122800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links