Variant report

Variant	rs1901363
Chromosome Location	chr8:99234481-99234482
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:99233406..99236750-chr8:99304645..99308471,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104361	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10955157	0.89[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10955158	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12542592	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12542593	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12542608	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12547555	0.92[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12549134	0.81[ASN][1000 genomes]
rs13263648	0.89[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2122929	0.90[ASN][1000 genomes]
rs3735884	0.84[ASN][1000 genomes]
rs55772672	1.00[ASN][1000 genomes]
rs55975205	0.81[ASN][1000 genomes]
rs62522241	0.86[ASN][1000 genomes]
rs62522242	0.86[ASN][1000 genomes]
rs62522245	0.86[ASN][1000 genomes]
rs62522247	1.00[ASN][1000 genomes]
rs62522248	1.00[ASN][1000 genomes]
rs62522249	1.00[ASN][1000 genomes]
rs6985720	0.84[ASN][1000 genomes]
rs6995263	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7005911	0.86[ASN][1000 genomes]
rs7016814	0.92[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[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	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv831405	chr8:99095239-99260934	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv6326	chr8:99221674-99263687	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1901363	NIPAL2	cis	cerebellum	SCAN
rs1901363	POP1	cis	cerebellum	SCAN
rs1901363	RAD54B	cis	cerebellum	SCAN
rs1901363	PLEKHF2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99191600-99243800	Weak transcription	Spleen	Spleen
2	chr8:99198200-99239200	Weak transcription	Lung	lung
3	chr8:99203800-99252600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr8:99205200-99259600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr8:99206600-99239800	Weak transcription	Pancreas	Pancrea
6	chr8:99211200-99243200	Weak transcription	Fetal Lung	lung
7	chr8:99213200-99239800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr8:99216600-99245400	Weak transcription	Stomach Mucosa	stomach
9	chr8:99217000-99234600	Weak transcription	Fetal Intestine Large	intestine
10	chr8:99217400-99238800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr8:99217800-99235000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr8:99217800-99238600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr8:99218400-99259000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr8:99220600-99234600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr8:99225200-99239800	Weak transcription	Gastric	stomach
16	chr8:99226000-99248400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr8:99226200-99246400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr8:99226200-99248400	Weak transcription	HSMMtube	muscle
19	chr8:99226200-99267000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr8:99226400-99245800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr8:99226400-99246200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr8:99226400-99246200	Weak transcription	Osteobl	bone
23	chr8:99228400-99234600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr8:99228800-99239000	Weak transcription	Ovary	ovary
25	chr8:99229400-99239200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr8:99229400-99239400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr8:99229400-99267000	Weak transcription	Left Ventricle	heart
28	chr8:99229600-99238800	Weak transcription	Aorta	Aorta
29	chr8:99229600-99241600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr8:99231000-99241200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr8:99231600-99238800	Weak transcription	Fetal Stomach	stomach
32	chr8:99231800-99238800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr8:99231800-99238800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr8:99232200-99234800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr8:99233000-99235200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr8:99233000-99245800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr8:99233200-99234800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr8:99233200-99235000	Weak transcription	NHEK	skin
39	chr8:99233400-99239200	Weak transcription	Esophagus	oesophagus
40	chr8:99233800-99235400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr8:99234400-99234800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr8:99234400-99235400	Strong transcription	Rectal Mucosa Donor 29	rectum

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