Variant report

Variant	rs4680460
Chromosome Location	chr3:158444215-158444216
allele	A/C
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	chr3:158433592..158436389-chr3:158442916..158446023,3	MCF-7	breast:
2	chr3:158381941..158384524-chr3:158442570..158444984,2	MCF-7	breast:
3	chr3:158439513..158442570-chr3:158443722..158446144,3	MCF-7	breast:
4	chr3:158443579..158445491-chr3:158458127..158461598,3	MCF-7	breast:
5	chr3:158370104..158372230-chr3:158443818..158446227,2	MCF-7	breast:
6	chr3:158425598..158427216-chr3:158443542..158445810,2	K562	blood:
7	chr3:158361077..158363871-chr3:158442170..158444537,2	MCF-7	breast:
8	chr3:158444127..158446205-chr3:158495477..158497180,2	K562	blood:
9	chr3:158440212..158445123-chr3:158504371..158509203,7	MCF-7	breast:
10	chr3:158438560..158442755-chr3:158443852..158445905,3	K562	blood:
11	chr3:158442646..158445031-chr3:158506699..158509425,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168827	Chromatin interaction
ENSG00000240207	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1006911	0.80[CHB][hapmap];0.90[YRI][hapmap];0.80[ASN][1000 genomes]
rs1047366	0.83[CEU][hapmap]
rs12639052	0.82[CEU][hapmap]
rs1346834	0.80[ASN][1000 genomes]
rs17699456	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1836688	0.82[GIH][hapmap]
rs1864507	0.83[CEU][hapmap]
rs1864508	0.80[ASN][1000 genomes]
rs2253249	0.80[CHB][hapmap];0.85[YRI][hapmap]
rs2303909	0.84[CEU][hapmap];0.80[GIH][hapmap]
rs2364927	0.85[ASN][1000 genomes]
rs2566346	1.00[ASN][1000 genomes]
rs3851362	0.82[CEU][hapmap]
rs4875	0.84[CEU][hapmap];0.84[GIH][hapmap]
rs57932243	0.86[ASN][1000 genomes]
rs61794797	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441224	0.89[ASN][1000 genomes]
rs6441225	0.80[CHB][hapmap];0.81[ASN][1000 genomes]
rs6772483	0.84[CEU][hapmap];0.80[GIH][hapmap]
rs6783879	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6800914	0.83[CEU][hapmap]
rs6803047	0.84[CEU][hapmap]
rs6804249	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7618110	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7621897	0.84[CEU][hapmap]
rs7631310	0.82[GIH][hapmap]
rs7635993	0.95[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];0.95[YRI][hapmap];0.87[ASN][1000 genomes]
rs8455	0.83[CEU][hapmap];0.80[GIH][hapmap]
rs891464	0.84[CEU][hapmap];0.80[GIH][hapmap]
rs9819567	0.84[CEU][hapmap]
rs9822005	0.90[YRI][hapmap]
rs9825696	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9840571	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9861938	0.95[CHB][hapmap];0.81[CHD][hapmap];0.87[ASN][1000 genomes]
rs9863103	0.95[CHB][hapmap];0.81[CHD][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs9866134	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9881462	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4680460	TIPARP	cis	cerebellum	SCAN
rs4680460	GFM1	cis	parietal	SCAN
rs4680460	RARRES1	cis	cerebellum	SCAN
rs4680460	LXN	cis	cerebellum	SCAN
rs4680460	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs4680460	LXN	cis	lymphoblastoid	seeQTL
rs4680460	GFM1	cis	cerebellum	SCAN
rs4680460	LXN	cis	parietal	SCAN
rs4680460	MLF1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158390800-158445400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr3:158397000-158448000	Weak transcription	Thymus	Thymus
3	chr3:158399600-158445400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:158424200-158446000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:158429600-158449000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:158431000-158445400	Weak transcription	GM12878-XiMat	blood
7	chr3:158431000-158449200	Weak transcription	Brain Germinal Matrix	brain
8	chr3:158431200-158445400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:158431200-158445800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:158431400-158445400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:158431400-158445400	Weak transcription	Dnd41	blood
12	chr3:158432000-158445400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:158432000-158445400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:158432200-158444800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:158432200-158445400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:158432200-158445800	Weak transcription	Brain Substantia Nigra	brain
17	chr3:158432200-158449200	Weak transcription	Pancreas	Pancrea
18	chr3:158435000-158449200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:158439200-158449200	Weak transcription	Fetal Brain Female	brain
20	chr3:158439600-158445400	Weak transcription	Fetal Kidney	kidney
21	chr3:158439800-158444600	Enhancers	Fetal Intestine Large	intestine
22	chr3:158439800-158445200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:158440000-158444800	Enhancers	Muscle Satellite Cultured Cells	--
24	chr3:158440200-158445800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:158440200-158445800	Weak transcription	Brain Anterior Caudate	brain
26	chr3:158440200-158446000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr3:158440600-158444400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:158440600-158445000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:158440600-158445400	Enhancers	NHLF	lung
30	chr3:158440600-158446000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:158440600-158446400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:158440800-158446200	Enhancers	NHDF-Ad	bronchial
33	chr3:158440800-158446800	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr3:158441000-158446000	Weak transcription	Fetal Brain Male	brain
35	chr3:158441000-158449200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:158441000-158449200	Weak transcription	Esophagus	oesophagus
37	chr3:158441200-158444400	Enhancers	Duodenum Mucosa	Duodenum
38	chr3:158441200-158445400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:158441200-158445800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr3:158441200-158445800	Genic enhancers	Fetal Intestine Small	intestine
41	chr3:158441200-158445800	Enhancers	Osteobl	bone
42	chr3:158441200-158446000	Enhancers	NH-A	brain
43	chr3:158441400-158445200	Weak transcription	Primary B cells from cord blood	blood
44	chr3:158441400-158445200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr3:158441400-158445400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr3:158441400-158445400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr3:158441400-158445600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:158441400-158449000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:158441600-158445200	Weak transcription	Primary T cells from cord blood	blood
50	chr3:158441600-158445400	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links