Variant report

Variant	rs62158585
Chromosome Location	chr2:113306827-113306828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr2:113306646-113306995	HepG2	liver:	n/a	n/a
2	FOXA1	chr2:113306555-113306950	HepG2	liver:	n/a	n/a
3	FOXA1	chr2:113306485-113306930	HepG2	liver:	n/a	n/a
4	FOXA2	chr2:113306643-113306942	HepG2	liver:	n/a	n/a
5	ARID3A	chr2:113306810-113306904	HepG2	liver:	n/a	n/a
6	JUND	chr2:113306657-113306876	HepG2	liver:	n/a	n/a
7	FOXA1	chr2:113306498-113307037	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113299867..113302656-chr2:113306781..113308489,3	MCF-7	breast:
2	chr2:113305772..113308199-chr2:113342160..113343764,2	MCF-7	breast:
3	chr2:113252098..113253969-chr2:113305095..113307068,2	MCF-7	breast:

No data

Variant related genes	Relation type
POLR1B	TF binding region
ENSG00000125611	Chromatin interaction
ENSG00000125630	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10169290	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10169344	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10183849	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10200067	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10205187	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13395691	0.90[ASN][1000 genomes]
rs13395779	0.90[ASN][1000 genomes]
rs13412193	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13413001	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13424021	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1583616	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2241804	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789724	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3961914	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59033131	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60489148	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60518507	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61669219	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158580	0.91[ASN][1000 genomes]
rs62158582	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158584	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62158586	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158591	0.95[ASN][1000 genomes]
rs62158643	0.91[ASN][1000 genomes]
rs62158644	0.90[ASN][1000 genomes]
rs7565714	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7565827	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9308671	0.85[ASN][1000 genomes]
rs9308672	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808491	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs62158585	POLR1B	cis	Whole Blood	GTEx
rs62158585	POLR1B	cis	Esophagus Muscularis	GTEx
rs62158585	POLR1B	cis	Adipose Subcutaneous	GTEx
rs62158585	POLR1B	cis	Thyroid	GTEx
rs62158585	POLR1B	cis	Artery Tibial	GTEx
rs62158585	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	chr2:113301200-113307200	Weak transcription	HSMMtube	muscle
2	chr2:113301200-113340200	Weak transcription	Right Atrium	heart
3	chr2:113301200-113341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:113301400-113308800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:113301400-113308800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:113301400-113310000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:113301400-113326200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:113301600-113307600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:113301600-113308800	Weak transcription	Small Intestine	intestine
10	chr2:113301600-113316800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:113301600-113316800	Weak transcription	Stomach Mucosa	stomach
12	chr2:113301600-113325400	Weak transcription	Fetal Brain Male	brain
13	chr2:113301600-113325400	Weak transcription	Fetal Heart	heart
14	chr2:113303000-113320200	Strong transcription	K562	blood
15	chr2:113303000-113325400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:113303000-113325600	Strong transcription	Primary T cells from cord blood	blood
17	chr2:113303000-113334400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:113303000-113334400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr2:113303000-113335200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:113303200-113313200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:113303200-113320200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:113303200-113334200	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:113303200-113334600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:113303400-113308200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:113303400-113320200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr2:113303400-113320200	Strong transcription	Fetal Intestine Large	intestine
27	chr2:113303400-113326200	Strong transcription	Primary B cells from cord blood	blood
28	chr2:113303400-113334400	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:113303400-113334600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:113303600-113311600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:113303600-113313400	Strong transcription	Brain Hippocampus Middle	brain
32	chr2:113303600-113314200	Strong transcription	NHEK	skin
33	chr2:113303600-113317000	Strong transcription	HUVEC	blood vessel
34	chr2:113303600-113317400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:113303600-113319800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:113303600-113320200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:113303600-113320400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:113303600-113320400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:113303600-113324400	Strong transcription	Fetal Brain Female	brain
40	chr2:113303600-113325400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:113303600-113325400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:113303600-113325800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:113303600-113326400	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr2:113303600-113326600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:113303600-113334000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr2:113303600-113334400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:113303600-113334400	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:113303600-113334400	Strong transcription	Fetal Muscle Trunk	muscle
49	chr2:113303600-113334600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:113303600-113334600	Strong transcription	HUES6 Cell Line	embryonic stem cell

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