Variant report

Variant	rs10471269
Chromosome Location	chr5:60575543-60575544
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	chr5:60458169..60460018-chr5:60573555..60575664,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188725	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10041973	0.84[AFR][1000 genomes]
rs10044683	1.00[CEU][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10070347	1.00[CEU][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10471511	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10939896	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12187377	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6869396	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6870703	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73103624	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9291719	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9291720	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv823088	chr5:60572580-60577406	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv441955	chr5:60573147-60576860	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60564600-60576000	Weak transcription	Psoas Muscle	Psoas
2	chr5:60567800-60577200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr5:60571200-60576600	Weak transcription	Pancreas	Pancrea
4	chr5:60571800-60583800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:60572000-60577000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:60572000-60582400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:60573400-60575600	Weak transcription	HSMM	muscle
8	chr5:60573400-60575800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:60573400-60575800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:60573400-60575800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:60573400-60586600	Weak transcription	Esophagus	oesophagus
12	chr5:60573400-60594800	Weak transcription	Right Atrium	heart
13	chr5:60573600-60575600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr5:60573600-60575600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr5:60573600-60575600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr5:60573600-60575600	Weak transcription	NH-A	brain
17	chr5:60573600-60575600	Weak transcription	Osteobl	bone
18	chr5:60573600-60575800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr5:60573600-60575800	Weak transcription	HSMMtube	muscle
20	chr5:60573600-60576000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:60573600-60576000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:60573600-60576000	Weak transcription	Colon Smooth Muscle	Colon
23	chr5:60573600-60576000	Weak transcription	Fetal Lung	lung
24	chr5:60573600-60576000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr5:60573600-60576000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr5:60573600-60576000	Weak transcription	Stomach Mucosa	stomach
27	chr5:60573600-60576000	Weak transcription	GM12878-XiMat	blood
28	chr5:60573600-60576200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:60573600-60576200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr5:60573600-60576200	Weak transcription	Brain Substantia Nigra	brain
31	chr5:60573800-60575600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr5:60573800-60575600	Weak transcription	HUVEC	blood vessel
33	chr5:60573800-60575600	Weak transcription	NHLF	lung
34	chr5:60573800-60575800	Weak transcription	A549	lung
35	chr5:60573800-60575800	Weak transcription	NHDF-Ad	bronchial
36	chr5:60573800-60576000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:60573800-60576200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr5:60573800-60576600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:60574000-60575600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr5:60574000-60575600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:60574000-60575800	Weak transcription	Primary B cells from cord blood	blood
42	chr5:60574000-60576200	Weak transcription	Brain Hippocampus Middle	brain
43	chr5:60574000-60576600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr5:60574000-60585400	Weak transcription	Spleen	Spleen
45	chr5:60574400-60575600	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr5:60574400-60575800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:60574400-60575800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:60574400-60575800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr5:60574600-60575600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:60574600-60576800	Enhancers	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links