Variant report

Variant	rs10053056
Chromosome Location	chr5:96043420-96043421
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96042717..96044579-chr5:96047527..96049294,2	K562	blood:
2	chr5:96036755..96041395-chr5:96042282..96045652,7	K562	blood:
3	chr5:96037082..96041395-chr5:96043344..96047377,11	K562	blood:

Variant related genes	Relation type
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10866771	0.84[AFR][1000 genomes]
rs11739478	0.82[CEU][hapmap];0.80[GIH][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap]
rs4434401	0.84[ASW][hapmap];0.82[CEU][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs4869306	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][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	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10053056	CAST	cis	parietal	SCAN
rs10053056	CAST	cis	cerebellum	SCAN
rs10053056	ERAP1	cis	cerebellum	SCAN
rs10053056	FAM81B	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96039200-96050600	Weak transcription	Gastric	stomach
2	chr5:96039200-96054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:96039200-96054400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:96039200-96054400	Weak transcription	Spleen	Spleen
5	chr5:96039200-96059800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:96039400-96050200	Weak transcription	Aorta	Aorta
7	chr5:96039600-96046200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr5:96039600-96063600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr5:96039800-96048000	Weak transcription	Pancreas	Pancrea
10	chr5:96039800-96049600	Weak transcription	Fetal Muscle Leg	muscle
11	chr5:96039800-96049800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:96040000-96044200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:96040000-96044200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr5:96040000-96044200	Weak transcription	Ovary	ovary
15	chr5:96040000-96044400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:96040000-96044400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:96040000-96044400	Weak transcription	A549	lung
18	chr5:96040000-96044400	Weak transcription	HSMM	muscle
19	chr5:96040000-96044600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:96040000-96044600	Weak transcription	NH-A	brain
21	chr5:96040000-96044800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:96040000-96046000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr5:96040000-96046600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:96040000-96047400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr5:96040000-96049600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr5:96040000-96049800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:96040000-96050000	Weak transcription	Primary T cells from cord blood	blood
28	chr5:96040000-96050000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:96040000-96050200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr5:96040000-96050400	Weak transcription	Primary B cells from cord blood	blood
31	chr5:96040000-96054400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:96040000-96054400	Weak transcription	Fetal Stomach	stomach
33	chr5:96040200-96044400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:96040200-96044400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr5:96040200-96044400	Weak transcription	Osteobl	bone
36	chr5:96040200-96046600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:96040200-96046800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr5:96040200-96049400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr5:96040200-96049800	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr5:96040200-96050200	Weak transcription	Brain Substantia Nigra	brain
41	chr5:96040200-96050600	Weak transcription	Brain Anterior Caudate	brain
42	chr5:96040400-96044600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr5:96040400-96044600	Weak transcription	HUVEC	blood vessel
44	chr5:96040400-96047200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr5:96040400-96049800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr5:96040600-96043600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr5:96040600-96044400	Weak transcription	Colon Smooth Muscle	Colon
48	chr5:96040600-96044600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:96040600-96044600	Weak transcription	Adipose Nuclei	Adipose
50	chr5:96040600-96046800	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links