Variant report

Variant	rs2307030
Chromosome Location	chr3:139066061-139066062
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:139065642-139069144	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139061660..139066893-chr3:139105523..139110764,11	K562	blood:
2	chr3:139063205..139066777-chr3:139105523..139110764,7	K562	blood:

Variant related genes	Relation type
MRPS22	TF binding region
ENSG00000184432	Chromatin interaction
ENSG00000252245	Chromatin interaction
ENSG00000248932	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10513077	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11914638	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11924964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928018	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12107249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1599926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182409	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs2233817	1.00[CEU][hapmap]
rs2278577	1.00[CEU][hapmap]
rs2289345	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2289346	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34994114	0.94[ASN][1000 genomes]
rs3772874	1.00[CEU][hapmap]
rs3772875	0.86[CEU][hapmap]
rs56176652	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57459537	0.81[ASN][1000 genomes]
rs57490542	0.94[ASN][1000 genomes]
rs60077646	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61613815	0.94[ASN][1000 genomes]
rs6439863	1.00[CEU][hapmap]
rs6767503	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770374	0.88[EUR][1000 genomes]
rs6773840	1.00[ASN][1000 genomes]
rs6774691	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6776315	1.00[CEU][hapmap]
rs6781318	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788896	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6797945	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72986758	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7373302	1.00[CEU][hapmap]
rs7612306	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7619827	0.85[AMR][1000 genomes]
rs7622961	1.00[JPT][hapmap]
rs7649535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9756378	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879736	1.00[CEU][hapmap]
rs9879748	1.00[CEU][hapmap]

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	nsv1005158	chr3:139001736-139073011	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	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
3	nsv4034	chr3:139034976-139080133	Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	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
5	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139063800-139070000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:139064000-139066400	Weak transcription	Placenta	Placenta
3	chr3:139064000-139067000	Weak transcription	Fetal Kidney	kidney
4	chr3:139064000-139070200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:139064000-139073400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:139064000-139073600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:139064000-139073600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:139064200-139066600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:139064200-139067200	Weak transcription	NHLF	lung
10	chr3:139064200-139068200	Weak transcription	Stomach Mucosa	stomach
11	chr3:139064200-139068200	Weak transcription	A549	lung
12	chr3:139064200-139072600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:139064200-139089200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:139064400-139097200	Strong transcription	Fetal Muscle Leg	muscle
15	chr3:139064600-139066400	Weak transcription	Fetal Brain Male	brain
16	chr3:139064600-139067000	Weak transcription	Ovary	ovary
17	chr3:139064600-139069600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:139064800-139066400	Genic enhancers	NHEK	skin
19	chr3:139064800-139068000	Weak transcription	NHDF-Ad	bronchial
20	chr3:139064800-139068600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:139064800-139068800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:139064800-139071200	Weak transcription	Fetal Heart	heart
23	chr3:139064800-139074800	Weak transcription	Right Atrium	heart
24	chr3:139064800-139094600	Strong transcription	Primary B cells from cord blood	blood
25	chr3:139065000-139066200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:139065000-139066200	Strong transcription	Aorta	Aorta
27	chr3:139065000-139067600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:139065000-139096200	Strong transcription	Fetal Intestine Large	intestine
29	chr3:139065000-139101200	Strong transcription	Primary T cells from cord blood	blood
30	chr3:139065000-139103800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:139065000-139103800	Strong transcription	HSMM	muscle
32	chr3:139065000-139104000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:139065200-139066200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:139065200-139066200	Weak transcription	GM12878-XiMat	blood
35	chr3:139065200-139066400	Weak transcription	Psoas Muscle	Psoas
36	chr3:139065200-139066600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:139065200-139066800	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:139065200-139069000	Weak transcription	Small Intestine	intestine
39	chr3:139065200-139073200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:139065200-139073200	Strong transcription	K562	blood
41	chr3:139065200-139089200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr3:139065200-139093600	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:139065200-139096800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:139065200-139098000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:139065200-139102000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr3:139065200-139102200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr3:139065400-139066600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr3:139065400-139067200	Strong transcription	Brain Hippocampus Middle	brain
49	chr3:139065400-139067600	Strong transcription	Hela-S3	cervix
50	chr3:139065400-139068400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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