Variant report

Variant	rs7552211
Chromosome Location	chr1:45523377-45523378
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45521218..45524154-chr1:45525277..45526789,2	K562	blood:
2	chr1:45478814..45481522-chr1:45521104..45523443,2	K562	blood:

Variant related genes	Relation type
ENSG00000126088	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11211075	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11211077	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11211080	0.95[EUR][1000 genomes]
rs1143726	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1143727	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1144866	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1144867	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1144870	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1144871	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1152017	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1152018	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1152020	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1152022	0.97[EUR][1000 genomes]
rs11585488	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs11588448	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1226722	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1226723	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1226727	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1226728	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1226736	0.92[EUR][1000 genomes]
rs1226740	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1226749	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1226912	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12750360	0.97[EUR][1000 genomes]
rs16832411	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1698295	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1938302	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1938406	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2211644	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2356304	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2883902	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2997400	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2997462	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3009973	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3009976	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3009978	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3121731	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3121770	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3128437	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3128443	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6429555	0.82[MKK][hapmap]
rs6429558	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6698681	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6700502	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs6702389	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs68139854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7517524	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7528468	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7548075	0.97[EUR][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	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
5	nsv546148	chr1:45500294-45627663	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7552211	SNORD55	cis	cerebellum	SCAN
rs7552211	SNORD55	cis	parietal	SCAN
rs7552211	ZNF691	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45481200-45525000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:45481200-45527400	Weak transcription	Left Ventricle	heart
3	chr1:45482000-45523800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:45497400-45525400	Weak transcription	Gastric	stomach
5	chr1:45498000-45525600	Weak transcription	Pancreas	Pancrea
6	chr1:45501800-45527000	Weak transcription	Fetal Brain Male	brain
7	chr1:45502000-45523800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:45504200-45524200	Weak transcription	Esophagus	oesophagus
9	chr1:45504400-45524000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:45505000-45526000	Weak transcription	Fetal Stomach	stomach
11	chr1:45507600-45527000	Weak transcription	Fetal Kidney	kidney
12	chr1:45509000-45523800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:45509000-45524000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:45509600-45526200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:45512400-45523800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:45513600-45525400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:45513600-45526200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:45517000-45525600	Weak transcription	Small Intestine	intestine
19	chr1:45517400-45526200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:45517600-45523400	Weak transcription	Fetal Intestine Large	intestine
21	chr1:45517600-45526800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:45517800-45525600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr1:45520400-45529200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:45521200-45525800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:45521200-45525800	Strong transcription	HepG2	liver
26	chr1:45521200-45526600	Strong transcription	Ovary	ovary
27	chr1:45521400-45525800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr1:45521400-45526000	Strong transcription	Brain Germinal Matrix	brain
29	chr1:45521400-45527400	Weak transcription	Fetal Intestine Small	intestine
30	chr1:45522200-45524800	Strong transcription	Brain Anterior Caudate	brain
31	chr1:45522400-45523400	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:45522400-45524800	Strong transcription	Stomach Smooth Muscle	stomach
33	chr1:45522600-45524600	Strong transcription	Brain Substantia Nigra	brain
34	chr1:45522600-45524600	Strong transcription	Duodenum Mucosa	Duodenum
35	chr1:45522600-45525800	Strong transcription	Brain Hippocampus Middle	brain
36	chr1:45522600-45526000	Strong transcription	Fetal Brain Female	brain
37	chr1:45522800-45524400	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:45523000-45523600	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr1:45523000-45523600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr1:45523000-45524600	Strong transcription	Aorta	Aorta
41	chr1:45523000-45525200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:45523000-45525200	Strong transcription	Brain Angular Gyrus	brain
43	chr1:45523000-45525400	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links