Variant report

Variant	rs13413001
Chromosome Location	chr2:113315803-113315804
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113315194..113318130-chr2:113339764..113342699,2	MCF-7	breast:
2	chr2:113306840..113309635-chr2:113313962..113316455,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125630	Chromatin interaction
ENSG00000125611	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10169290	0.90[ASN][1000 genomes]
rs10169344	0.90[ASN][1000 genomes]
rs10183849	0.90[ASN][1000 genomes]
rs10200067	0.91[ASN][1000 genomes]
rs10205187	0.90[ASN][1000 genomes]
rs13395691	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13395779	0.91[ASN][1000 genomes]
rs13412193	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13424021	0.98[ASN][1000 genomes]
rs1583616	0.98[ASN][1000 genomes]
rs2241804	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3748026	0.82[AMR][1000 genomes]
rs3789724	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3961914	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57339041	0.82[AMR][1000 genomes]
rs59033131	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60489148	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60518507	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61669219	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62158580	0.91[ASN][1000 genomes]
rs62158582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62158584	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62158585	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62158586	0.87[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	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7565714	0.86[ASN][1000 genomes]
rs7565827	0.86[ASN][1000 genomes]
rs9308671	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9308672	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9808491	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13413001	POLR1B	cis	Esophagus Muscularis	GTEx
rs13413001	POLR1B	cis	Thyroid	GTEx
rs13413001	POLR1B	cis	Artery Tibial	GTEx
rs13413001	POLR1B	cis	Whole Blood	GTEx
rs13413001	POLR1B	cis	Adipose Subcutaneous	GTEx
rs13413001	POLR1B	cis	Stomach	GTEx
rs13413001	POLR1B	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113301200-113340200	Weak transcription	Right Atrium	heart
2	chr2:113301200-113341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:113301400-113326200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:113301600-113316800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:113301600-113316800	Weak transcription	Stomach Mucosa	stomach
6	chr2:113301600-113325400	Weak transcription	Fetal Brain Male	brain
7	chr2:113301600-113325400	Weak transcription	Fetal Heart	heart
8	chr2:113303000-113320200	Strong transcription	K562	blood
9	chr2:113303000-113325400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:113303000-113325600	Strong transcription	Primary T cells from cord blood	blood
11	chr2:113303000-113334400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:113303000-113334400	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr2:113303000-113335200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:113303200-113320200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:113303200-113334200	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:113303200-113334600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:113303400-113320200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr2:113303400-113320200	Strong transcription	Fetal Intestine Large	intestine
19	chr2:113303400-113326200	Strong transcription	Primary B cells from cord blood	blood
20	chr2:113303400-113334400	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:113303400-113334600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:113303600-113317000	Strong transcription	HUVEC	blood vessel
23	chr2:113303600-113317400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:113303600-113319800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:113303600-113320200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:113303600-113320400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:113303600-113320400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:113303600-113324400	Strong transcription	Fetal Brain Female	brain
29	chr2:113303600-113325400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:113303600-113325400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:113303600-113325800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:113303600-113326400	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr2:113303600-113326600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr2:113303600-113334000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr2:113303600-113334400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:113303600-113334400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr2:113303600-113334400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr2:113303600-113334600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:113303600-113334600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:113303600-113334800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:113303600-113334800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:113303600-113335000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:113303600-113335000	Strong transcription	Fetal Thymus	thymus
44	chr2:113303600-113335200	Strong transcription	Fetal Muscle Leg	muscle
45	chr2:113303800-113334800	Strong transcription	Duodenum Mucosa	Duodenum
46	chr2:113304000-113327800	Strong transcription	Dnd41	blood
47	chr2:113304400-113320400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr2:113304400-113333600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:113304400-113334200	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr2:113304400-113334400	Strong transcription	Sigmoid Colon	Sigmoid Colon

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