Variant report

Variant	rs11583244
Chromosome Location	chr1:225952474-225952475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225948785..225952549-chr1:225953599..225956527,4	MCF-7	breast:
2	chr1:225950876..225953793-chr1:225964413..225967358,3	K562	blood:
3	chr1:225834091..225845547-chr1:225952149..225961130,23	MCF-7	breast:
4	chr1:225952293..225956105-chr1:225956557..225960824,5	MCF-7	breast:
5	chr1:225838129..225843793-chr1:225950745..225961465,25	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143742	Chromatin interaction
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12403575	0.83[EUR][1000 genomes]
rs2794399	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34653791	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4653431	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653671	0.83[EUR][1000 genomes]
rs6670903	0.83[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	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats 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 miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225943600-225954800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:225946200-225959800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:225946600-225955400	Weak transcription	Fetal Intestine Large	intestine
4	chr1:225949400-225952600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:225949600-225952800	Enhancers	Fetal Muscle Trunk	muscle
6	chr1:225949600-225954000	Enhancers	Fetal Lung	lung
7	chr1:225949600-225960400	Enhancers	Fetal Muscle Leg	muscle
8	chr1:225949800-225954600	Weak transcription	Brain Substantia Nigra	brain
9	chr1:225950000-225955000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:225950200-225952600	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr1:225950200-225953200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:225950200-225953600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:225950400-225952600	Enhancers	Aorta	Aorta
14	chr1:225950400-225954200	Weak transcription	K562	blood
15	chr1:225950400-225955200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:225950600-225954200	Weak transcription	Fetal Kidney	kidney
17	chr1:225950600-225955000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:225950600-225955000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:225950600-225955000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:225950600-225955200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:225950600-225955200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:225950600-225955400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:225950600-225957200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:225950600-225958200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:225950800-225955200	Weak transcription	Fetal Intestine Small	intestine
26	chr1:225951200-225952600	Enhancers	Lung	lung
27	chr1:225951200-225952600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr1:225951200-225952600	Enhancers	Spleen	Spleen
29	chr1:225951800-225953600	Weak transcription	HepG2	liver
30	chr1:225951800-225955000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:225951800-225955000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:225952000-225952600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:225952000-225952600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:225952000-225952600	Enhancers	HUVEC	blood vessel
35	chr1:225952000-225952800	Enhancers	Primary B cells from peripheral blood	blood
36	chr1:225952000-225952800	Enhancers	Stomach Smooth Muscle	stomach
37	chr1:225952000-225954200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:225952000-225954400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr1:225952000-225954800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:225952200-225952600	Enhancers	Adipose Nuclei	Adipose
41	chr1:225952200-225952600	Enhancers	Rectal Smooth Muscle	rectum
42	chr1:225952200-225952600	Enhancers	Osteobl	bone
43	chr1:225952200-225953000	Weak transcription	Left Ventricle	heart
44	chr1:225952200-225953600	Weak transcription	Fetal Thymus	thymus
45	chr1:225952200-225954000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:225952200-225954000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:225952200-225954000	Weak transcription	Fetal Brain Male	brain
48	chr1:225952200-225954200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:225952200-225954200	Weak transcription	Brain Anterior Caudate	brain
50	chr1:225952200-225954200	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links