Variant report

Variant	rs4855884
Chromosome Location	chr3:49704077-49704078
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	chr3:49701796..49704696-chr3:49705542..49707912,3	MCF-7	breast:
2	chr3:49572703..49574370-chr3:49703529..49706014,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1050088	0.85[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs1060962	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130199	0.85[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap]
rs11130212	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130213	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1131095	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap]
rs11709525	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.81[ASN][1000 genomes]
rs11710037	0.81[ASN][1000 genomes]
rs11718165	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11919311	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12490267	0.87[EUR][1000 genomes]
rs12497288	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13085791	1.00[CHB][hapmap]
rs13316695	0.81[ASN][1000 genomes]
rs1352890	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1568661	0.85[CHD][hapmap];0.94[GIH][hapmap]
rs1801143	0.85[GIH][hapmap]
rs1826347	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs1873625	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap]
rs1873626	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2005557	1.00[CEU][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131104	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131109	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2172252	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2329020	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2960548	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3197999	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap]
rs34762726	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs35007338	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35404120	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35701831	0.85[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs3811697	0.85[GIH][hapmap]
rs3870338	0.85[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs3924462	0.85[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs4283605	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs4625	0.85[GIH][hapmap]
rs4855835	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4855839	0.85[CHD][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap]
rs4855847	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4855852	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4855859	0.85[CHD][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs4855864	0.85[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs4855881	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4855883	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6765869	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766131	0.85[GIH][hapmap]
rs6767878	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6770670	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6782577	0.96[CEU][hapmap]
rs6803222	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap]
rs7622302	0.85[GIH][hapmap]
rs7637999	0.85[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs9812791	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[ASN][1000 genomes]
rs9822268	0.92[CHD][hapmap];0.88[GIH][hapmap]
rs9823546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9824092	0.81[ASN][1000 genomes]
rs9827708	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap]
rs9836291	0.91[ASN][1000 genomes]
rs9837027	0.85[GIH][hapmap]
rs9837341	1.00[CHB][hapmap]
rs9853683	0.85[GIH][hapmap]
rs9858213	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9858280	0.85[GIH][hapmap]
rs9858542	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9862080	0.81[ASN][1000 genomes]
rs9875617	0.85[GIH][hapmap]
rs9882740	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4855884	IP6K2	cis	cerebellum	SCAN
rs4855884	ALS2CL	cis	cerebellum	SCAN
rs4855884	CISH	cis	lymphoblastoid	seeQTL
rs4855884	CELSR3	cis	cerebellum	SCAN
rs4855884	CCDC71	cis	cerebellum	SCAN
rs4855884	ARIH2	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49685200-49708200	Strong transcription	Brain Germinal Matrix	brain
2	chr3:49685400-49708400	Strong transcription	Fetal Brain Female	brain
3	chr3:49686600-49710600	Weak transcription	Right Atrium	heart
4	chr3:49687600-49705800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:49690400-49710600	Weak transcription	Brain Substantia Nigra	brain
6	chr3:49692200-49710400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49695200-49710600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:49700000-49710600	Weak transcription	Fetal Brain Male	brain
9	chr3:49700800-49704400	Strong transcription	Brain Anterior Caudate	brain
10	chr3:49701400-49704800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:49701800-49707000	Enhancers	Fetal Muscle Leg	muscle
12	chr3:49702000-49704600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:49702000-49707400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:49702400-49705600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:49702400-49710600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:49702600-49704400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:49702800-49704400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:49702800-49707400	Enhancers	Pancreas	Pancrea
19	chr3:49703000-49704600	Flanking Active TSS	HepG2	liver
20	chr3:49703200-49704200	Enhancers	Gastric	stomach
21	chr3:49703400-49705200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:49703400-49709400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:49703600-49704400	Weak transcription	Brain Angular Gyrus	brain
24	chr3:49703600-49704400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:49703600-49704800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr3:49703600-49705200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr3:49703600-49705200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:49703600-49705800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:49703600-49706200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:49703600-49709000	Weak transcription	Placenta	Placenta
31	chr3:49703600-49710600	Weak transcription	Left Ventricle	heart
32	chr3:49703600-49710600	Weak transcription	Right Ventricle	heart
33	chr3:49703600-49710600	Weak transcription	Spleen	Spleen
34	chr3:49703800-49705400	Weak transcription	HMEC	breast
35	chr3:49703800-49705600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:49703800-49706000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:49703800-49710600	Enhancers	Liver	Liver
38	chr3:49703800-49710600	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:49704000-49704200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:49704000-49704400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:49704000-49704600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:49704000-49704600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr3:49704000-49704800	Enhancers	Fetal Intestine Small	intestine
44	chr3:49704000-49705200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:49704000-49706800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:49704000-49707000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin

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