Variant report

Variant	rs955948
Chromosome Location	chr5:80608266-80608267
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:80597031..80598832-chr5:80606167..80608882,2	K562	blood:
2	chr5:80599729..80604075-chr5:80605851..80609625,4	K562	blood:
3	chr5:80599288..80602129-chr5:80607036..80608849,2	K562	blood:
4	chr5:80607330..80608887-chr5:80610841..80612586,2	K562	blood:

Variant related genes	Relation type
ENSG00000131732	Chromatin interaction
ENSG00000247572	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10041138	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10052929	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1039326	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs12514420	0.86[ASN][1000 genomes]
rs12652649	0.84[CHB][hapmap];0.90[EUR][1000 genomes]
rs13159978	0.83[EUR][1000 genomes]
rs1566433	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2406557	0.86[ASN][1000 genomes]
rs4502795	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4704713	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4704714	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs56938600	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57266451	0.83[ASN][1000 genomes]
rs59563495	0.83[EUR][1000 genomes]
rs6863732	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6868743	0.83[ASN][1000 genomes]
rs6871676	0.80[ASN][1000 genomes]
rs6889795	0.83[ASN][1000 genomes]
rs6896441	0.83[ASN][1000 genomes]
rs6896890	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7731117	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs871701	0.83[JPT][hapmap]

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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80598200-80612400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:80598400-80611200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:80598600-80608800	Weak transcription	Brain Germinal Matrix	brain
4	chr5:80598600-80609600	Weak transcription	Gastric	stomach
5	chr5:80598600-80610000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:80598600-80611200	Weak transcription	Brain Anterior Caudate	brain
7	chr5:80598600-80611200	Weak transcription	Fetal Brain Male	brain
8	chr5:80598600-80611200	Weak transcription	Small Intestine	intestine
9	chr5:80598600-80611200	Weak transcription	Stomach Mucosa	stomach
10	chr5:80598600-80611800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:80598800-80611000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:80598800-80611200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:80599200-80610000	Weak transcription	Pancreas	Pancrea
14	chr5:80599200-80612200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:80599400-80610400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:80599600-80609200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr5:80599600-80610600	Weak transcription	Fetal Heart	heart
18	chr5:80599600-80611200	Weak transcription	Brain Substantia Nigra	brain
19	chr5:80599800-80608400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr5:80599800-80611400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr5:80601400-80611000	Weak transcription	Hela-S3	cervix
22	chr5:80601400-80612400	Weak transcription	Colon Smooth Muscle	Colon
23	chr5:80601400-80612400	Weak transcription	Thymus	Thymus
24	chr5:80601600-80611000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:80601600-80611200	Weak transcription	Colonic Mucosa	Colon
26	chr5:80601600-80611200	Weak transcription	Spleen	Spleen
27	chr5:80601600-80611600	Weak transcription	Esophagus	oesophagus
28	chr5:80601800-80610000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:80602000-80609800	Weak transcription	K562	blood
30	chr5:80604000-80609800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:80604200-80610000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:80604200-80610000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr5:80604200-80611200	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr5:80604200-80611400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:80604200-80611600	Strong transcription	Primary T cells from cord blood	blood
36	chr5:80604400-80608400	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr5:80604400-80608400	Strong transcription	NHEK	skin
38	chr5:80604400-80608600	Strong transcription	Fetal Intestine Large	intestine
39	chr5:80604400-80608600	Strong transcription	Psoas Muscle	Psoas
40	chr5:80604400-80608800	Strong transcription	Fetal Muscle Leg	muscle
41	chr5:80604400-80609200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:80604400-80609800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:80604400-80610000	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr5:80604400-80610000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:80604400-80610000	Strong transcription	Duodenum Mucosa	Duodenum
46	chr5:80604400-80610200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:80604400-80610200	Strong transcription	HSMM	muscle
48	chr5:80604400-80610400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:80604400-80610600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr5:80604400-80610600	Strong transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links