Variant report

Variant	rs4849186
Chromosome Location	chr2:113999534-113999535
allele	C/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	MAX	chr2:113998216-113999609	SK-N-SH	brain:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
2	POLR2A	chr2:113998335-114000919	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr2:113997003-114000128	IMR90	lung:	n/a	n/a
4	FOSL2	chr2:113997326-113999659	A549	lung:	n/a	chr2:113999384-113999396 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113998585-113998596 chr2:113999386-113999394
5	E2F6	chr2:113998475-113999603	A549	lung:	n/a	n/a
6	E2F6	chr2:113998194-113999726	A549	lung:	n/a	n/a
7	POLR2A	chr2:113998495-113999803	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr2:113996944-114000866	K562	blood:	n/a	n/a
9	POLR2A	chr2:113999302-114000351	GM12878	blood:	n/a	n/a
10	MAX	chr2:113999371-113999575	HepG2	liver:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
11	MYC	chr2:113999409-113999548	K562	blood:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
12	MAX	chr2:113996927-113999829	A549	lung:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
13	FOSL1	chr2:113997636-113999713	HCT-116	colon:	n/a	chr2:113999384-113999396 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113999386-113999394
14	POLR2A	chr2:113999028-113999775	HCT-116	colon:	n/a	n/a
15	MYC	chr2:113997694-113999664	MCF10A-Er-Src	breast:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
16	CEBPB	chr2:113997572-113999797	HCT-116	colon:	n/a	chr2:113998825-113998836
17	POLR2A	chr2:113999465-113999641	GM12878	blood:	n/a	n/a
18	POLR2A	chr2:113999527-113999688	GM12878	blood:	n/a	n/a
19	TCF12	chr2:113997522-113999698	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr2:113997465-113999660	U87	brain:	n/a	n/a
21	POLR2A	chr2:113997633-113999727	HCT-116	colon:	n/a	n/a
22	FOSL2	chr2:113997572-113999623	SK-N-SH	brain:	n/a	chr2:113999384-113999396 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113998585-113998596 chr2:113999386-113999394
23	FOSL1	chr2:113997637-113999745	HCT-116	colon:	n/a	chr2:113999384-113999396 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113999386-113999394
24	USF1	chr2:113999186-113999550	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr2:113998349-114000010	K562	blood:	n/a	n/a
26	USF1	chr2:113999238-113999610	K562	blood:	n/a	n/a
27	SP1	chr2:113997449-113999766	HCT-116	colon:	n/a	n/a
28	JUND	chr2:113997591-113999665	HCT-116	colon:	n/a	chr2:113999384-113999396 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113998584-113998595 chr2:113999385-113999395 chr2:113999386-113999394
29	MAX	chr2:113999219-113999590	K562	blood:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
30	MAX	chr2:113999251-113999685	ECC-1	luminal epithelium:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
31	MAX	chr2:113999315-113999546	K562	blood:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
32	POLR2A	chr2:113997148-113999795	U87	brain:	n/a	n/a
33	BHLHE40	chr2:113999451-113999589	K562	blood:	n/a	n/a
34	POLR2A	chr2:113997148-113999542	U87	brain:	n/a	n/a
35	SP1	chr2:113997517-113999763	HCT-116	colon:	n/a	n/a
36	MAX	chr2:113997190-113999788	A549	lung:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
37	SIN3AK20	chr2:113997576-113999649	HCT-116	colon:	n/a	n/a
38	JUND	chr2:113997644-113999673	HCT-116	colon:	n/a	chr2:113999384-113999396 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113998584-113998595 chr2:113999385-113999395 chr2:113999386-113999394
39	MYC	chr2:113997825-113999568	MCF10A-Er-Src	breast:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
40	USF1	chr2:113999135-113999771	HCT-116	colon:	n/a	n/a
41	MAX	chr2:113997553-113999839	HCT-116	colon:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
42	USF2	chr2:113999300-113999598	Hela-S3	cervix:	n/a	chr2:113999415-113999426 chr2:113999455-113999466
43	POLR2A	chr2:113998357-114000456	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr2:113997531-114000147	K562	blood:	n/a	n/a
45	MAX	chr2:113997744-113999561	A549	lung:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
46	MAZ	chr2:113996918-113999877	IMR90	lung:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
47	CEBPB	chr2:113997577-113999695	HCT-116	colon:	n/a	chr2:113998825-113998836
48	MAX	chr2:113997526-113999827	HCT-116	colon:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
49	FOS	chr2:113997829-113999549	MCF10A-Er-Src	breast:	n/a	chr2:113999384-113999396 chr2:113998584-113998595 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113999386-113999394

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113950220..113951864-chr2:113997428..113999954,2	K562	blood:
2	chr2:113954862..113956783-chr2:113998620..114001129,2	MCF-7	breast:

Variant related genes	Relation type
PAX8	TF binding region
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1021409	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12467324	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12471722	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12998725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13015478	0.90[CEU][hapmap]
rs2003986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2018348	0.86[CEU][hapmap]
rs2863242	1.00[YRI][hapmap]
rs3738913	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4848320	0.81[AMR][1000 genomes]
rs4849178	1.00[YRI][hapmap]
rs745912	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459008	chr2:113972945-114010791	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv582713	chr2:113972945-114010791	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4849186	AC016683.6	cis	Whole Blood	GTEx
rs4849186	AC016683.6	cis	lung	GTEx
rs4849186	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs4849186	PAX8	cis	lung	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113993400-114000000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:113993400-114006600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:113994200-114002000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:113994200-114006600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:113994600-114000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:113994800-114006600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:113995000-114006800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:113995200-114000000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr2:113995200-114007000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:113995600-114000200	Weak transcription	Dnd41	blood
11	chr2:113995600-114008600	Weak transcription	GM12878-XiMat	blood
12	chr2:113996600-114000200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:113997000-113999600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:113997000-113999600	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr2:113997000-114000000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:113997000-114000000	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr2:113997000-114000000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr2:113997000-114000600	Enhancers	Esophagus	oesophagus
19	chr2:113997200-113999600	Enhancers	Stomach Mucosa	stomach
20	chr2:113997400-113999600	Enhancers	Fetal Stomach	stomach
21	chr2:113997400-113999600	Enhancers	Left Ventricle	heart
22	chr2:113997400-113999800	Enhancers	Right Ventricle	heart
23	chr2:113997400-114000200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr2:113997600-113999600	Enhancers	Ovary	ovary
25	chr2:113997600-113999800	Enhancers	Fetal Intestine Large	intestine
26	chr2:113997600-114001000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr2:113998000-113999800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:113998000-113999800	Enhancers	Lung	lung
29	chr2:113998200-113999600	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr2:113998200-113999600	Enhancers	Stomach Smooth Muscle	stomach
31	chr2:113998200-114000200	Enhancers	Adipose Nuclei	Adipose
32	chr2:113998200-114000200	Enhancers	HMEC	breast
33	chr2:113998200-114000800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:113998200-114006600	Weak transcription	Fetal Thymus	thymus
35	chr2:113998200-114020600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:113998400-113999600	Enhancers	Brain Hippocampus Middle	brain
37	chr2:113998400-113999600	Enhancers	Brain Substantia Nigra	brain
38	chr2:113998400-113999600	Enhancers	HSMMtube	muscle
39	chr2:113998400-113999800	Enhancers	NH-A	brain
40	chr2:113998400-114000000	Enhancers	HSMM	muscle
41	chr2:113998600-113999600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:113998600-113999600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:113998600-113999800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr2:113998600-113999800	Enhancers	NHLF	lung
45	chr2:113998600-114000000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr2:113998600-114000200	Enhancers	Fetal Heart	heart
47	chr2:113998600-114000200	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr2:113998600-114000200	Enhancers	NHDF-Ad	bronchial
49	chr2:113998600-114000200	Enhancers	NHEK	skin
50	chr2:113998600-114000800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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