Variant report

Variant	rs13412193
Chromosome Location	chr2:113301727-113301728
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr2:113298346-113301743	SK-N-SH	brain:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113300113..113302309-chr2:113304266..113305973,2	MCF-7	breast:
2	chr2:113298569..113302646-chr2:113339335..113343133,7	K562	blood:
3	chr2:113296892..113302637-chr2:113340004..113344909,8	K562	blood:
4	chr2:113298759..113301838-chr2:113339526..113343252,4	MCF-7	breast:
5	chr2:113297047..113302352-chr2:113483159..113487384,5	K562	blood:
6	chr2:113299867..113302656-chr2:113306781..113308489,3	MCF-7	breast:
7	chr2:112640408..112642506-chr2:113299856..113302341,2	K562	blood:
8	chr2:113235916..113241390-chr2:113298151..113302275,12	MCF-7	breast:
9	chr2:113031538..113036695-chr2:113297613..113301921,6	K562	blood:
10	chr2:113298954..113302477-chr2:113339455..113343767,5	MCF-7	breast:
11	chr2:113238895..113243312-chr2:113297571..113302127,8	K562	blood:
12	chr2:113235572..113240260-chr2:113300212..113305167,6	MCF-7	breast:

No data

Variant related genes	Relation type
POLR1B	TF binding region
ENSG00000125630	Chromatin interaction
ENSG00000153107	Chromatin interaction
ENSG00000144130	Chromatin interaction
ENSG00000188177	Chromatin interaction
ENSG00000125611	Chromatin interaction
ENSG00000114999	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10169290	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10169344	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10183849	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10200067	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10205187	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12469608	0.81[JPT][hapmap]
rs13395691	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.90[ASN][1000 genomes]
rs13395779	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.91[ASN][1000 genomes]
rs13413001	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13424021	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1583616	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2241804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34179430	0.81[JPT][hapmap]
rs3748026	1.00[CEU][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs3789724	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3961914	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59033131	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60489148	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60518507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61669219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62158580	0.91[ASN][1000 genomes]
rs62158582	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62158584	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62158585	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62158586	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62158591	0.96[ASN][1000 genomes]
rs62158643	0.90[ASN][1000 genomes]
rs62158644	0.89[ASN][1000 genomes]
rs7559710	0.81[JPT][hapmap]
rs7565714	0.84[CHB][hapmap];0.80[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7565827	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7576952	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs9308671	0.86[ASN][1000 genomes]
rs9308672	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9808491	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13412193	POLR1B	cis	Adipose Subcutaneous	GTEx
rs13412193	POLR1B	cis	Thyroid	GTEx
rs13412193	POLR1B	cis	Nerve Tibial	GTEx
rs13412193	POLR1B	cis	Whole Blood	GTEx
rs13412193	POLR1B	cis	Esophagus Muscularis	GTEx
rs13412193	POLR1B	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113298600-113303600	Active TSS	GM12878-XiMat	blood
2	chr2:113299400-113302400	Active TSS	Hela-S3	cervix
3	chr2:113300200-113301800	Flanking Active TSS	Dnd41	blood
4	chr2:113300600-113301800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:113301000-113301800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:113301000-113301800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr2:113301000-113301800	Flanking Active TSS	NHEK	skin
8	chr2:113301000-113304600	Weak transcription	Aorta	Aorta
9	chr2:113301200-113301800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:113301200-113301800	Enhancers	Primary B cells from cord blood	blood
11	chr2:113301200-113301800	Enhancers	Primary B cells from peripheral blood	blood
12	chr2:113301200-113301800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr2:113301200-113301800	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr2:113301200-113301800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:113301200-113301800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:113301200-113301800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:113301200-113301800	Enhancers	Adipose Nuclei	Adipose
18	chr2:113301200-113301800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr2:113301200-113301800	Enhancers	Fetal Muscle Trunk	muscle
20	chr2:113301200-113302800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:113301200-113303800	Weak transcription	Brain Substantia Nigra	brain
22	chr2:113301200-113304400	Weak transcription	Colonic Mucosa	Colon
23	chr2:113301200-113304600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:113301200-113304600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:113301200-113304600	Weak transcription	Fetal Stomach	stomach
26	chr2:113301200-113304600	Weak transcription	Right Ventricle	heart
27	chr2:113301200-113305000	Weak transcription	NH-A	brain
28	chr2:113301200-113307200	Weak transcription	HSMMtube	muscle
29	chr2:113301200-113340200	Weak transcription	Right Atrium	heart
30	chr2:113301200-113341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr2:113301400-113301800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:113301400-113301800	Enhancers	Primary T cells fromperipheralblood	blood
33	chr2:113301400-113301800	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr2:113301400-113301800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:113301400-113301800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:113301400-113301800	Flanking Active TSS	HepG2	liver
37	chr2:113301400-113302000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:113301400-113302400	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr2:113301400-113302400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:113301400-113302800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:113301400-113303200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:113301400-113303600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:113301400-113303600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr2:113301400-113304400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr2:113301400-113304600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:113301400-113304600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:113301400-113304600	Weak transcription	Thymus	Thymus
48	chr2:113301400-113304800	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:113301400-113304800	Weak transcription	Fetal Kidney	kidney
50	chr2:113301400-113308800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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