Variant report

Variant	rs974801
Chromosome Location	chr4:106071064-106071065
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:56707907..56710968-chr4:106067665..106071186,3	MCF-7	breast:
2	chr4:105789109..105790890-chr4:106069609..106071424,2	MCF-7	breast:
3	chr4:105812145..105831361-chr4:106062414..106073665,101	MCF-7	breast:
4	chr4:106069706..106072401-chr4:106190053..106191894,2	K562	blood:
5	chr4:106070612..106071326-chrX:2821056..2821740,2	MCF-7	breast:
6	chr4:106070265..106072695-chr4:106079640..106082370,2	K562	blood:
7	chr4:106070816..106072685-chr4:106394532..106396510,2	MCF-7	breast:
8	chr4:105981331..105982913-chr4:106070883..106073179,2	MCF-7	breast:
9	chr4:105883010..105897017-chr4:106062943..106072055,55	MCF-7	breast:
10	chr4:105884036..105898505-chr4:106054854..106072562,138	MCF-7	breast:
11	chr4:105849643..105852121-chr4:106070083..106072880,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000138777	Chromatin interaction
ENSG00000248242	Chromatin interaction
ENSG00000248373	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000251906	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10014102	0.96[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10022109	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12641113	0.91[ASN][1000 genomes]
rs12643257	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12645165	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12647922	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1391440	0.81[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs17583558	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17617028	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2189234	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2285720	0.96[CEU][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28493806	0.85[EUR][1000 genomes]
rs2903386	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs62331150	0.88[ASN][1000 genomes]
rs62331151	0.99[ASN][1000 genomes]
rs9790517	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9884482	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs974801	PPA2	cis	cerebellum	SCAN
rs974801	NPNT	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106064800-106071800	Active TSS	GM12878-XiMat	blood
2	chr4:106068400-106071200	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr4:106069200-106071400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr4:106069200-106071400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:106069400-106071800	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr4:106069400-106071800	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr4:106069400-106072000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:106069400-106072000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr4:106069400-106083200	Weak transcription	Pancreas	Pancrea
10	chr4:106069400-106087600	Weak transcription	Lung	lung
11	chr4:106069400-106114200	Weak transcription	Esophagus	oesophagus
12	chr4:106069600-106071400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:106069600-106073200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr4:106069600-106102400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:106069800-106071200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr4:106069800-106071800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr4:106069800-106071800	Enhancers	Hela-S3	cervix
18	chr4:106069800-106072000	Enhancers	Brain Angular Gyrus	brain
19	chr4:106069800-106072000	Enhancers	HepG2	liver
20	chr4:106069800-106072400	Enhancers	Fetal Heart	heart
21	chr4:106069800-106072400	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr4:106069800-106075600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:106069800-106075800	Weak transcription	Aorta	Aorta
24	chr4:106069800-106080000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:106069800-106080200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr4:106069800-106101000	Weak transcription	HSMM	muscle
27	chr4:106069800-106101800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr4:106070000-106071400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:106070000-106072000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:106070000-106072200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr4:106070000-106072400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr4:106070000-106072600	Enhancers	Adipose Nuclei	Adipose
33	chr4:106070200-106071200	Enhancers	Liver	Liver
34	chr4:106070200-106076000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:106070200-106076400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:106070200-106076800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr4:106070200-106080600	Weak transcription	Fetal Stomach	stomach
38	chr4:106070400-106071200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:106070400-106071200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:106070400-106071600	Weak transcription	HSMMtube	muscle
41	chr4:106070400-106071800	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr4:106070400-106071800	Enhancers	Fetal Intestine Small	intestine
43	chr4:106070400-106071800	Enhancers	NHEK	skin
44	chr4:106070400-106072000	Enhancers	Brain Hippocampus Middle	brain
45	chr4:106070400-106072000	Enhancers	Brain Substantia Nigra	brain
46	chr4:106070400-106072000	Enhancers	Fetal Intestine Large	intestine
47	chr4:106070400-106072000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr4:106070400-106072400	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr4:106070400-106107800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:106070400-106111600	Weak transcription	Placenta	Placenta

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