Variant report

Variant	rs1563688
Chromosome Location	chr4:89765009-89765010
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	chr4:89763902..89766661-chr4:89768609..89770489,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10001319	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022272	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10028121	0.82[CHB][hapmap]
rs11097200	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735482	1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1379934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1708673	0.82[CHB][hapmap]
rs2100679	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2125410	0.82[CHB][hapmap]
rs2609254	0.82[CHB][hapmap]
rs2609263	0.82[CHB][hapmap]
rs2609274	0.82[CHB][hapmap]
rs2704593	0.82[CHB][hapmap]
rs2869965	0.82[CHB][hapmap]
rs34321014	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62308743	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7680357	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89745000-89770800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:89745000-89775000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:89745200-89776200	Weak transcription	Aorta	Aorta
4	chr4:89749000-89769600	Weak transcription	K562	blood
5	chr4:89752000-89778800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:89752800-89769200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:89754600-89779600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:89756400-89767400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:89761600-89767400	Weak transcription	HepG2	liver
10	chr4:89763000-89767400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:89763200-89765200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:89763200-89765400	Enhancers	Fetal Lung	lung
13	chr4:89763400-89765200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:89763400-89765400	Enhancers	Stomach Mucosa	stomach
15	chr4:89763400-89766000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr4:89763600-89765200	Enhancers	Small Intestine	intestine
17	chr4:89763600-89766200	Enhancers	Fetal Intestine Small	intestine
18	chr4:89764000-89765200	Enhancers	HUVEC	blood vessel
19	chr4:89764200-89765400	Enhancers	Fetal Intestine Large	intestine
20	chr4:89764400-89765200	Enhancers	Adipose Nuclei	Adipose
21	chr4:89764400-89765200	Enhancers	Fetal Heart	heart
22	chr4:89764400-89765200	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr4:89764400-89765400	Strong transcription	Placenta	Placenta
24	chr4:89764400-89765800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:89764400-89766000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:89764400-89767600	Weak transcription	NHLF	lung
27	chr4:89764400-89779400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr4:89764600-89769800	Weak transcription	NH-A	brain
29	chr4:89764800-89765200	Enhancers	Fetal Muscle Leg	muscle
30	chr4:89764800-89766000	Enhancers	Pancreas	Pancrea
31	chr4:89764800-89767000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:89764800-89769200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:89765000-89765200	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr4:89765000-89765400	Enhancers	Gastric	stomach
35	chr4:89765000-89765400	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr4:89765000-89766600	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr4:89765000-89766800	Weak transcription	Osteobl	bone
38	chr4:89765000-89767400	Weak transcription	NHDF-Ad	bronchial
39	chr4:89765000-89773200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:89765000-89779400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:89765000-89780400	Weak transcription	Ovary	ovary
42	chr4:89765000-89780600	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links