Variant report

Variant	rs3772881
Chromosome Location	chr3:139174933-139174934
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	chr3:139174418..139175114-chr3:139280608..139281156,2	MCF-7	breast:
2	chr3:139168645..139171256-chr3:139173067..139176313,3	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1017469	0.84[EUR][1000 genomes]
rs10935322	0.96[CEU][hapmap]
rs10935326	0.81[EUR][1000 genomes]
rs10935328	0.85[EUR][1000 genomes]
rs10935331	0.89[ASW][hapmap]
rs11705700	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs11706576	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs11721246	0.85[EUR][1000 genomes]
rs11920890	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs11928377	0.85[EUR][1000 genomes]
rs12495890	0.85[EUR][1000 genomes]
rs13064670	0.83[EUR][1000 genomes]
rs13313904	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs13316469	0.84[EUR][1000 genomes]
rs13326837	0.96[CEU][hapmap]
rs13327467	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs13434189	0.96[CEU][hapmap]
rs1371338	0.85[EUR][1000 genomes]
rs1371339	0.85[EUR][1000 genomes]
rs1550352	0.85[EUR][1000 genomes]
rs1583743	0.96[CEU][hapmap];0.83[GIH][hapmap];0.82[EUR][1000 genomes]
rs1586862	0.96[CEU][hapmap]
rs17395255	0.96[CEU][hapmap]
rs17395304	0.96[CEU][hapmap]
rs1817830	0.85[EUR][1000 genomes]
rs1817831	0.85[EUR][1000 genomes]
rs188422	0.92[CEU][hapmap]
rs2118980	0.85[EUR][1000 genomes]
rs2289347	0.85[EUR][1000 genomes]
rs2289349	0.85[EUR][1000 genomes]
rs2349058	0.85[EUR][1000 genomes]
rs28771131	0.85[EUR][1000 genomes]
rs28780368	0.80[EUR][1000 genomes]
rs28829348	0.85[EUR][1000 genomes]
rs28861812	0.85[EUR][1000 genomes]
rs295486	0.88[CEU][hapmap]
rs3555	0.85[EUR][1000 genomes]
rs35674260	0.96[CEU][hapmap];0.83[GIH][hapmap];0.82[EUR][1000 genomes]
rs4428138	0.85[EUR][1000 genomes]
rs444264	0.96[CEU][hapmap];0.83[GIH][hapmap]
rs4547659	0.85[EUR][1000 genomes]
rs62270815	0.83[EUR][1000 genomes]
rs62270816	0.84[EUR][1000 genomes]
rs6439858	0.84[EUR][1000 genomes]
rs6439861	0.85[EUR][1000 genomes]
rs6439862	0.96[CEU][hapmap];0.83[GIH][hapmap];0.85[EUR][1000 genomes]
rs6778992	0.84[EUR][1000 genomes]
rs6801875	0.85[EUR][1000 genomes]
rs6804877	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7372124	0.96[CEU][hapmap];0.80[GIH][hapmap]
rs7372551	0.83[EUR][1000 genomes]
rs7372811	0.96[CEU][hapmap]
rs7372813	0.85[EUR][1000 genomes]
rs7373116	0.96[CEU][hapmap]
rs7374065	0.85[EUR][1000 genomes]
rs7374317	0.92[CEU][hapmap]
rs7374348	0.96[CEU][hapmap]
rs7433335	0.85[EUR][1000 genomes]
rs7612112	0.85[EUR][1000 genomes]
rs7616025	0.83[EUR][1000 genomes]
rs7626658	0.84[EUR][1000 genomes]
rs7627718	0.83[EUR][1000 genomes]
rs7645307	0.85[EUR][1000 genomes]
rs7833	0.96[CEU][hapmap]
rs878535	0.85[EUR][1000 genomes]
rs964226	0.85[EUR][1000 genomes]
rs978835	0.96[CEU][hapmap];0.83[GIH][hapmap];0.84[EUR][1000 genomes]
rs9812991	0.85[EUR][1000 genomes]
rs9813503	0.85[EUR][1000 genomes]
rs9817963	0.85[EUR][1000 genomes]
rs9819368	0.96[CEU][hapmap]
rs9821875	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs9821891	0.96[CEU][hapmap]
rs9828954	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs9831144	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs9833460	0.85[EUR][1000 genomes]
rs9839681	0.85[EUR][1000 genomes]
rs9848820	0.84[EUR][1000 genomes]
rs9848959	0.85[EUR][1000 genomes]
rs9849255	0.85[EUR][1000 genomes]
rs9850987	0.96[CEU][hapmap]
rs9851318	0.96[CEU][hapmap]
rs9857390	0.96[CEU][hapmap]
rs9859393	0.85[EUR][1000 genomes]
rs9871030	0.96[CEU][hapmap]
rs9872749	0.85[EUR][1000 genomes]
rs9873011	0.85[EUR][1000 genomes]
rs9874227	0.85[EUR][1000 genomes]
rs9876640	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs9881973	0.84[EUR][1000 genomes]
rs9990108	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1000519	chr3:139159300-139206245	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2752377	chr3:139163302-139188302	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3772881	MRPS22	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139142800-139176800	Weak transcription	Fetal Stomach	stomach
2	chr3:139154200-139178600	Weak transcription	Left Ventricle	heart
3	chr3:139163400-139189000	Weak transcription	Small Intestine	intestine
4	chr3:139163800-139180200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:139165800-139178600	Weak transcription	Right Ventricle	heart
6	chr3:139166000-139179000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:139167000-139175400	Weak transcription	Fetal Brain Female	brain
8	chr3:139167400-139176000	Weak transcription	Brain Anterior Caudate	brain
9	chr3:139168000-139175200	Weak transcription	Brain Angular Gyrus	brain
10	chr3:139168600-139196000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:139169200-139175000	Genic enhancers	Fetal Intestine Small	intestine
12	chr3:139171200-139210200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:139171400-139175800	Weak transcription	Brain Substantia Nigra	brain
14	chr3:139171400-139179400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr3:139171400-139179400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:139171800-139176000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:139171800-139176200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:139172000-139175600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:139172000-139176200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr3:139172000-139176200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr3:139172200-139175400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr3:139172400-139175400	Enhancers	H9 Cell Line	embryonic stem cell
23	chr3:139172400-139177000	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr3:139172600-139175200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr3:139173400-139175000	Enhancers	Brain Germinal Matrix	brain
26	chr3:139173400-139175600	Genic enhancers	Fetal Intestine Large	intestine
27	chr3:139173800-139175400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:139173800-139178400	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:139173800-139180600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:139173800-139180600	Weak transcription	Pancreas	Pancrea
31	chr3:139174200-139176800	Enhancers	Ovary	ovary
32	chr3:139174600-139176200	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr3:139174600-139177200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:139174800-139175000	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr3:139174800-139175000	Enhancers	Esophagus	oesophagus
36	chr3:139174800-139175200	Enhancers	Fetal Brain Male	brain
37	chr3:139174800-139175400	Enhancers	Adipose Nuclei	Adipose
38	chr3:139174800-139175600	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr3:139174800-139176400	Enhancers	Brain Cingulate Gyrus	brain
40	chr3:139174800-139176800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:139174800-139176800	Enhancers	HMEC	breast
42	chr3:139174800-139177000	Enhancers	NHEK	skin
43	chr3:139174800-139177200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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