Variant report

Variant	rs13431315
Chromosome Location	chr2:113997294-113997295
allele	C/T
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	POLR2A	chr2:113997003-114000128	IMR90	lung:	n/a	n/a
2	POLR2A	chr2:113996944-114000866	K562	blood:	n/a	n/a
3	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
4	TCF12	chr2:113997289-113998206	ECC-1	luminal epithelium:	n/a	n/a
5	JUND	chr2:113997140-113999306	SK-N-SH	brain:	n/a	chr2:113998584-113998595
6	POLR2A	chr2:113997058-113997626	HCT-116	colon:	n/a	n/a
7	EP300	chr2:113997276-113999114	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr2:113997154-113997508	K562	blood:	n/a	n/a
9	GATA3	chr2:113997238-113999374	A549	lung:	n/a	n/a
10	POLR2A	chr2:113997148-113999795	U87	brain:	n/a	n/a
11	POLR2A	chr2:113997148-113999542	U87	brain:	n/a	n/a
12	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
13	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

No.	Distal block	Cell Line	Cell type
1	chr2:113952804..113954880-chr2:113996400..113999228,2	MCF-7	breast:
2	chr2:113958931..113961853-chr2:113995609..113998129,2	K562	blood:
3	chr2:113970934..113973261-chr2:113995727..113997421,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSD4-1	chr2:113996666-113998402	ENSG00000189223
2	lnc-PSD4-1	chr2:113996666-113997485	ENSG00000189223
3	lnc-PSD4-1	chr2:113996666-113998419	NONHSAT073761

Variant related genes	Relation type
PAX8	TF binding region
ENSG00000258395	TF binding region
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13405033	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35836064	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45449699	0.87[ASN][1000 genomes]
rs66775912	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67081417	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67776659	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67802835	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831810	0.81[AMR][1000 genomes];0.87[EUR][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

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113984000-113998000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:113992000-113997400	Weak transcription	Left Ventricle	heart
3	chr2:113992000-113997400	Weak transcription	Right Ventricle	heart
4	chr2:113993400-113997400	Weak transcription	HUVEC	blood vessel
5	chr2:113993400-114000000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:113993400-114006600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr2:113993600-113997400	Weak transcription	Brain Angular Gyrus	brain
8	chr2:113994200-114002000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:113994200-114006600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:113994400-113997600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:113994400-113997800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:113994600-113997400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:113994600-113997400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:113994600-113998000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:113994600-113998000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:113994600-114000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:113994800-113997400	Weak transcription	Fetal Stomach	stomach
18	chr2:113994800-113997600	Weak transcription	Ovary	ovary
19	chr2:113994800-113998000	Weak transcription	Fetal Brain Female	brain
20	chr2:113994800-113998600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:113994800-114006600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr2:113995000-113998200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:113995000-113998800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:113995000-114006800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:113995200-113997600	Enhancers	Adipose Nuclei	Adipose
26	chr2:113995200-113997800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr2:113995200-114000000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr2:113995200-114007000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr2:113995400-113997400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:113995400-113997400	Weak transcription	Fetal Brain Male	brain
31	chr2:113995400-113998000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr2:113995400-113999000	Enhancers	Fetal Muscle Leg	muscle
33	chr2:113995600-113997400	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:113995600-113997400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr2:113995600-114000200	Weak transcription	Dnd41	blood
36	chr2:113995600-114008600	Weak transcription	GM12878-XiMat	blood
37	chr2:113995800-113997400	Enhancers	NHEK	skin
38	chr2:113995800-113997600	Genic enhancers	HSMM	muscle
39	chr2:113995800-113999000	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr2:113996200-113998200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr2:113996200-113998800	Genic enhancers	Fetal Kidney	kidney
42	chr2:113996400-113997600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:113996600-113997600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:113996600-114000200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:113996800-113997400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:113996800-113997600	Enhancers	Brain Hippocampus Middle	brain
47	chr2:113996800-113997600	Enhancers	HMEC	breast
48	chr2:113996800-113997800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:113996800-113998400	Enhancers	HepG2	liver
50	chr2:113996800-113998600	Enhancers	Fetal Muscle Trunk	muscle

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