Variant report

Variant	rs2250127
Chromosome Location	chr5:127388844-127388845
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:127388500..127392194-chr5:127417986..127422177,4	K562	blood:
2	chr5:127388145..127392194-chr5:127417181..127420286,4	K562	blood:

Variant related genes	Relation type
ENSG00000245937	Chromatin interaction
ENSG00000064651	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1112956	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11948128	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17764730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1993878	0.94[CEU][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs2409110	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568928	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2617617	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34576922	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3749748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6860245	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6888037	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6889311	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7734927	0.93[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs790154	0.87[CEU][hapmap]
rs790155	0.87[CEU][hapmap]
rs9327468	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813981	chr5:127327649-127437401	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv1806594	chr5:127336033-127410767	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv1808488	chr5:127336033-127410767	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv1825228	chr5:127336033-127410767	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv1829119	chr5:127336033-127410767	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv508378	chr5:127374904-127405030	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2250127	CTC-228N24.3	cis	Muscle Skeletal	GTEx
rs2250127	FLJ33630	Cis_1M	lymphoblastoid	RTeQTL
rs2250127	CTC-228N24.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2250127	CTC-228N24.3	cis	Thyroid	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127333600-127417800	Weak transcription	Pancreas	Pancrea
2	chr5:127334600-127394000	Weak transcription	Lung	lung
3	chr5:127335000-127397600	Weak transcription	NHDF-Ad	bronchial
4	chr5:127353200-127397000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:127354000-127397400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr5:127354400-127398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:127354600-127409800	Weak transcription	Left Ventricle	heart
8	chr5:127356200-127399200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr5:127356400-127414000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr5:127357200-127393800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr5:127358800-127389000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:127360400-127393800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr5:127366000-127389000	Weak transcription	HSMMtube	muscle
14	chr5:127369400-127398000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:127371600-127389000	Weak transcription	Psoas Muscle	Psoas
16	chr5:127371600-127398000	Weak transcription	Small Intestine	intestine
17	chr5:127373000-127389000	Weak transcription	Brain Angular Gyrus	brain
18	chr5:127374600-127418000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr5:127375200-127389000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:127375200-127414400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr5:127375800-127391000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:127376000-127397000	Weak transcription	NHEK	skin
23	chr5:127376400-127397400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:127376400-127414400	Weak transcription	Dnd41	blood
25	chr5:127377000-127391000	Weak transcription	Fetal Muscle Leg	muscle
26	chr5:127377200-127414200	Weak transcription	K562	blood
27	chr5:127378000-127416600	Weak transcription	Spleen	Spleen
28	chr5:127378400-127401600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr5:127378400-127414200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr5:127378800-127415800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr5:127379000-127417400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr5:127380000-127390200	Weak transcription	Right Ventricle	heart
33	chr5:127380000-127390800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr5:127380200-127398000	Weak transcription	Esophagus	oesophagus
35	chr5:127380200-127414600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr5:127380200-127416200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr5:127380400-127402800	Weak transcription	Gastric	stomach
38	chr5:127381000-127393800	Weak transcription	Ovary	ovary
39	chr5:127384600-127389000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:127384600-127397600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr5:127384800-127397800	Weak transcription	Brain Hippocampus Middle	brain
42	chr5:127385400-127398000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr5:127385600-127398000	Weak transcription	Brain Substantia Nigra	brain
44	chr5:127385600-127400000	Weak transcription	Fetal Lung	lung
45	chr5:127385800-127390000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr5:127386400-127390000	Weak transcription	Fetal Stomach	stomach
47	chr5:127386400-127395600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr5:127386400-127414400	Weak transcription	Colon Smooth Muscle	Colon
49	chr5:127386600-127389000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:127386600-127391200	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links