Variant report

Variant	rs2653574
Chromosome Location	chr11:8938124-8938125
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	chr11:8931316..8934225-chr11:8937249..8940014,3	K562	blood:
2	chr11:8932851..8934873-chr11:8937588..8939434,2	K562	blood:

Variant related genes	Relation type
ENSG00000166444	Chromatin interaction
ENSG00000166452	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10840170	1.00[CHB][hapmap]
rs1133833	0.83[GIH][hapmap];0.81[MEX][hapmap]
rs1136966	1.00[CHB][hapmap]
rs1984775	1.00[CHB][hapmap]
rs2568078	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2653558	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2742502	0.83[GIH][hapmap];0.85[MEX][hapmap]
rs34105455	1.00[ASN][1000 genomes]
rs34581555	1.00[ASN][1000 genomes]
rs34769330	1.00[ASN][1000 genomes]
rs3850934	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4061640	1.00[CHB][hapmap]
rs4910443	1.00[CHB][hapmap]
rs6486061	0.82[MEX][hapmap]
rs6486138	1.00[CHB][hapmap]
rs7396115	1.00[CHB][hapmap]
rs7396840	1.00[CHB][hapmap]
rs7936201	1.00[CHB][hapmap];0.81[MEX][hapmap]
rs7941341	1.00[CHB][hapmap]
rs7949022	1.00[CHB][hapmap]
rs7950491	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2653574	SCUBE2	cis	cerebellum	SCAN
rs2653574	AMPD3	cis	cerebellum	SCAN
rs2653574	AMPD3	cis	parietal	SCAN
rs2653574	RPL27A	cis	parietal	SCAN
rs2653574	RPL27A	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8933400-8947800	Weak transcription	Small Intestine	intestine
2	chr11:8933600-8944000	Weak transcription	Pancreas	Pancrea
3	chr11:8934000-8941800	Weak transcription	Colonic Mucosa	Colon
4	chr11:8934000-8952200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:8934200-8938400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:8934200-8941600	Weak transcription	Esophagus	oesophagus
7	chr11:8934200-8948800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:8934800-8939400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:8935000-8938200	Weak transcription	Psoas Muscle	Psoas
10	chr11:8935000-8940400	Genic enhancers	Fetal Muscle Leg	muscle
11	chr11:8935800-8940000	Weak transcription	Gastric	stomach
12	chr11:8936000-8938200	Weak transcription	Right Ventricle	heart
13	chr11:8936000-8938400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:8936000-8939600	Weak transcription	Fetal Brain Male	brain
15	chr11:8936000-8942800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr11:8936200-8938200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:8936200-8938200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr11:8936200-8938200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr11:8936200-8939200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr11:8936200-8945800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr11:8936400-8938200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr11:8936400-8938200	Weak transcription	Brain Germinal Matrix	brain
23	chr11:8936400-8938200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr11:8936400-8938800	Weak transcription	Primary B cells from cord blood	blood
25	chr11:8936400-8938800	Weak transcription	Aorta	Aorta
26	chr11:8936400-8941800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr11:8936400-8946000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr11:8936400-8946800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:8936400-8951200	Weak transcription	Right Atrium	heart
30	chr11:8936600-8938200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr11:8936600-8938200	Weak transcription	Primary T cells from cord blood	blood
32	chr11:8936600-8938200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:8936600-8938200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:8936600-8938200	Weak transcription	Fetal Heart	heart
35	chr11:8936600-8938200	Weak transcription	Spleen	Spleen
36	chr11:8936600-8938400	Weak transcription	Fetal Kidney	kidney
37	chr11:8936600-8939000	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr11:8936600-8940600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:8936600-8940800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr11:8936600-8941400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr11:8936600-8941600	Weak transcription	Ovary	ovary
42	chr11:8936600-8945000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr11:8936600-8945800	Weak transcription	Stomach Mucosa	stomach
44	chr11:8936600-8946600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr11:8936600-8948600	Strong transcription	Fetal Thymus	thymus
46	chr11:8936600-8949000	Strong transcription	Fetal Stomach	stomach
47	chr11:8936600-8954000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr11:8936800-8938200	Weak transcription	Brain Anterior Caudate	brain
49	chr11:8936800-8938200	Weak transcription	Brain Substantia Nigra	brain
50	chr11:8936800-8938200	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links