Variant report

Variant	rs4849092
Chromosome Location	chr2:113409225-113409226
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:113408045-113411294	A549	lung:	n/a	n/a
2	POLR2A	chr2:113409059-113409256	MCF-7	breast:	n/a	n/a
3	POLR2A	chr2:113409071-113410130	GM12892	blood:	n/a	n/a
4	TEAD4	chr2:113408220-113409280	K562	blood:	n/a	n/a
5	POLR2A	chr2:113408076-113409239	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:113409171-113409262	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:113408882-113410046	GM12892	blood:	n/a	n/a
8	POLR2A	chr2:113408936-113409236	K562	blood:	n/a	n/a
9	POLR2A	chr2:113401765-113425023	U87	brain:	n/a	n/a
10	POLR2A	chr2:113408908-113409972	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr2:113407109-113411432	K562	blood:	n/a	n/a
12	POLR2A	chr2:113408946-113409954	GM12892	blood:	n/a	n/a
13	POLR2A	chr2:113402016-113412293	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr2:113409053-113409897	GM12892	blood:	n/a	n/a
15	POLR2A	chr2:113407120-113411345	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr2:113407730-113411364	K562	blood:	n/a	n/a
17	POLR2A	chr2:113409197-113410397	HL-60	blood:	n/a	n/a
18	POLR2A	chr2:113408019-113411441	U87	brain:	n/a	n/a
19	POLR2A	chr2:113409219-113409252	MCF-7	breast:	n/a	n/a
20	POLR2A	chr2:113409100-113409256	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:113401943-113419910	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr2:113408797-113409322	K562	blood:	n/a	n/a
23	POLR2A	chr2:113408904-113409355	K562	blood:	n/a	n/a
24	POLR2A	chr2:113409005-113409550	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr2:113401765-113425014	U87	brain:	n/a	n/a
26	POLR2A	chr2:113409120-113409320	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr2:113409197-113409627	HCT-116	colon:	n/a	n/a
28	POLR2A	chr2:113401719-113411441	U87	brain:	n/a	n/a
29	PML	chr2:113407975-113411407	K562	blood:	n/a	n/a
30	POLR2A	chr2:113409212-113411376	K562	blood:	n/a	n/a
31	POLR2A	chr2:113408067-113411376	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:113362689..113364237-chr2:113407440..113409332,2	K562	blood:
2	chr2:113408007..113410255-chr2:113479531..113481072,2	K562	blood:
3	chr2:113401171..113414378-chr2:113468812..113486672,46	K562	blood:

No data

Variant related genes	Relation type
SLC20A1	TF binding region
ENSG00000144130	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10177499	0.82[EUR][1000 genomes]
rs10199279	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1061254	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10746527	0.82[AMR][1000 genomes]
rs10779886	0.82[AMR][1000 genomes]
rs11123144	0.84[EUR][1000 genomes]
rs11123145	0.87[AFR][1000 genomes]
rs13023311	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2312699	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3936697	0.84[EUR][1000 genomes]
rs4630766	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4848286	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4849087	0.83[EUR][1000 genomes]
rs4849088	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4849089	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4849090	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4849093	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4849094	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4849095	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4849096	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4849100	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6737094	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6747638	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6747928	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6751117	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6793	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7558138	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs885346	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

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	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
2	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
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4849092	AC079922.3	cis	Whole Blood	GTEx
rs4849092	AC079922.3	cis	Muscle Skeletal	GTEx
rs4849092	AC079922.3	cis	Heart Left Ventricle	GTEx
rs4849092	AC079922.3	cis	Nerve Tibial	GTEx
rs4849092	AC079922.3	cis	Artery Aorta	GTEx
rs4849092	AC079922.3	cis	Thyroid	GTEx
rs4849092	AC079922.3	cis	Esophagus Muscularis	GTEx
rs4849092	AC079922.3	cis	lung	GTEx
rs4849092	AC079922.3	cis	Esophagus Mucosa	GTEx
rs4849092	AC079922.3	cis	Artery Tibial	GTEx
rs4849092	AC079922.3	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113404000-113409600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:113404400-113410600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:113404600-113409800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:113404800-113412600	Weak transcription	Gastric	stomach
5	chr2:113404800-113414400	Weak transcription	Esophagus	oesophagus
6	chr2:113404800-113416200	Weak transcription	Ovary	ovary
7	chr2:113404800-113416800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:113405000-113409400	Weak transcription	Spleen	Spleen
9	chr2:113405000-113411200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:113405000-113413200	Strong transcription	Placenta	Placenta
11	chr2:113405000-113416200	Weak transcription	Aorta	Aorta
12	chr2:113405000-113416400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:113405000-113423200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:113405200-113411600	Strong transcription	Fetal Intestine Large	intestine
15	chr2:113405200-113413600	Strong transcription	Left Ventricle	heart
16	chr2:113405200-113419000	Weak transcription	Stomach Mucosa	stomach
17	chr2:113405200-113423200	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr2:113405200-113423800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr2:113405400-113409600	Weak transcription	Brain Substantia Nigra	brain
20	chr2:113405400-113412000	Strong transcription	Primary B cells from cord blood	blood
21	chr2:113405400-113412600	Weak transcription	Pancreas	Pancrea
22	chr2:113405400-113422600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr2:113405400-113423200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:113405400-113423200	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:113405600-113410000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr2:113405600-113411000	Strong transcription	Psoas Muscle	Psoas
27	chr2:113405600-113411600	Strong transcription	Primary hematopoietic stem cells	blood
28	chr2:113405600-113422000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:113405800-113411000	Genic enhancers	Liver	Liver
30	chr2:113405800-113422600	Strong transcription	Fetal Muscle Leg	muscle
31	chr2:113406000-113414600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:113406000-113419600	Strong transcription	Fetal Lung	lung
33	chr2:113406000-113423000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:113406200-113410400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:113406200-113410400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:113406200-113423400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:113406200-113423400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:113406200-113423600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:113406200-113424600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:113406400-113409400	Weak transcription	Fetal Kidney	kidney
41	chr2:113406400-113409800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr2:113406400-113414400	Weak transcription	Right Ventricle	heart
43	chr2:113406400-113423000	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr2:113406400-113423000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:113406400-113423200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr2:113406600-113409600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr2:113406600-113409800	Strong transcription	Fetal Stomach	stomach
48	chr2:113406800-113411800	Strong transcription	Brain Angular Gyrus	brain
49	chr2:113406800-113412800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:113406800-113423200	Strong transcription	Rectal Mucosa Donor 29	rectum

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