Variant report

Variant	rs12463996
Chromosome Location	chr2:113486879-113486880
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr2:113486832-113487404	HL-60	blood:	n/a	chr2:113487011-113487024 chr2:113487072-113487079

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113401788..113407326-chr2:113480776..113487899,15	MCF-7	breast:
2	chr2:113297047..113302352-chr2:113483159..113487384,5	K562	blood:
3	chr2:113484246..113487026-chr2:113487818..113491393,4	MCF-7	breast:
4	chr2:113415099..113418730-chr2:113484170..113487314,3	K562	blood:
5	chr2:113340008..113343992-chr2:113483304..113487579,6	K562	blood:
6	chr2:113482871..113484637-chr2:113485555..113488424,2	K562	blood:
7	chr2:113338959..113342918-chr2:113483353..113487579,5	K562	blood:
8	chr2:113485399..113487990-chr2:113522114..113523918,2	K562	blood:

No data

Variant related genes	Relation type
NT5DC4	TF binding region
ENSG00000237753	Chromatin interaction
ENSG00000144130	Chromatin interaction
ENSG00000125611	Chromatin interaction
ENSG00000169607	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000125630	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10165537	0.94[ASN][1000 genomes]
rs10193063	0.93[ASN][1000 genomes]
rs10200192	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10203064	0.93[ASN][1000 genomes]
rs11123149	0.94[ASN][1000 genomes]
rs12475027	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12622683	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13013602	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13015273	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13016817	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13019249	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13026263	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13036237	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13382217	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13429613	0.98[ASN][1000 genomes]
rs17649681	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2138606	0.82[EUR][1000 genomes]
rs2862226	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3811040	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3827761	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4261731	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4848298	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4849118	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55762606	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58694576	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6706663	0.94[ASN][1000 genomes]
rs6712572	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6721044	0.94[ASN][1000 genomes]
rs6721292	0.92[ASN][1000 genomes]
rs6753803	0.94[ASN][1000 genomes]
rs7577241	0.94[ASN][1000 genomes]
rs7591704	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7594852	0.82[EUR][1000 genomes]
rs7599690	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7607470	0.82[EUR][1000 genomes];0.91[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	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
2	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
3	nsv526301	chr2:113451498-113495785	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113477600-113487000	Enhancers	Monocytes-CD14+_RO01746	blood
2	chr2:113478600-113488200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:113480000-113488200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr2:113481200-113487600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr2:113483000-113488200	Enhancers	Spleen	Spleen
6	chr2:113483600-113487600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:113483800-113488200	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr2:113484000-113487400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr2:113484200-113497200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:113484400-113494200	Weak transcription	A549	lung
11	chr2:113484400-113494800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:113484400-113495000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:113484400-113495600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:113484400-113495600	Weak transcription	Thymus	Thymus
15	chr2:113484400-113495800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:113484400-113495800	Weak transcription	GM12878-XiMat	blood
17	chr2:113484400-113496400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:113484400-113507400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:113484600-113494200	Weak transcription	Fetal Thymus	thymus
20	chr2:113484600-113507600	Weak transcription	Colonic Mucosa	Colon
21	chr2:113484800-113490000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:113484800-113490400	Weak transcription	Fetal Brain Male	brain
23	chr2:113484800-113490400	Weak transcription	Fetal Intestine Large	intestine
24	chr2:113484800-113494400	Weak transcription	NHEK	skin
25	chr2:113484800-113494600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:113484800-113494800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:113484800-113495600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:113484800-113496200	Weak transcription	NHDF-Ad	bronchial
29	chr2:113484800-113507600	Weak transcription	Primary B cells from cord blood	blood
30	chr2:113485000-113494800	Weak transcription	Dnd41	blood
31	chr2:113485200-113494800	Weak transcription	HMEC	breast
32	chr2:113485400-113487600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:113486000-113487000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:113486000-113487200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:113486000-113491000	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:113486200-113487400	Enhancers	Adipose Nuclei	Adipose
37	chr2:113486200-113494400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:113486200-113494600	Weak transcription	Fetal Stomach	stomach
39	chr2:113486200-113495000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:113486400-113487400	Enhancers	Lung	lung
41	chr2:113486400-113490600	Weak transcription	Fetal Lung	lung
42	chr2:113486400-113491200	Weak transcription	Fetal Heart	heart
43	chr2:113486400-113495800	Weak transcription	HUVEC	blood vessel
44	chr2:113486600-113488200	Weak transcription	K562	blood
45	chr2:113486600-113496200	Weak transcription	Placenta	Placenta
46	chr2:113486600-113511600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links