Variant report

Variant	rs13003670
Chromosome Location	chr2:153549819-153549820
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	chr2:153549773-153549956	ProgFib	skin:	n/a	n/a
2	BCL11A	chr2:153549647-153549842	GM12878	blood:	n/a	n/a
3	NFIC	chr2:153549453-153550108	GM12878	blood:	n/a	n/a
4	EBF1	chr2:153549642-153549939	GM12878	blood:	n/a	n/a
5	NFATC1	chr2:153549500-153549928	GM12878	blood:	n/a	n/a
6	RUNX3	chr2:153549489-153550050	GM12878	blood:	n/a	n/a
7	RUNX3	chr2:153549478-153550085	GM12878	blood:	n/a	n/a
8	JUND	chr2:153549512-153549888	GM12878	blood:	n/a	n/a
9	BCLAF1	chr2:153549496-153550079	GM12878	blood:	n/a	n/a
10	BHLHE40	chr2:153549581-153549978	GM12878	blood:	n/a	n/a
11	EBF1	chr2:153549662-153550004	GM12878	blood:	n/a	n/a
12	FOXM1	chr2:153549520-153549907	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:153549391-153550761	K562	blood:	n/a	n/a
14	IRF4	chr2:153549452-153549980	GM12878	blood:	n/a	n/a
15	ATF2	chr2:153549462-153549969	GM12878	blood:	n/a	n/a
16	NFIC	chr2:153549349-153550083	GM12878	blood:	n/a	n/a
17	BATF	chr2:153549521-153549852	GM12878	blood:	n/a	chr2:153549696-153549707
18	IKZF1	chr2:153549589-153550048	GM12878	blood:	n/a	n/a
19	MEF2A	chr2:153549453-153549981	GM12878	blood:	n/a	n/a
20	ATF2	chr2:153549453-153550014	GM12878	blood:	n/a	n/a
21	BATF	chr2:153549437-153549936	GM12878	blood:	n/a	chr2:153549696-153549707
22	BCL3	chr2:153549570-153549887	GM12878	blood:	n/a	n/a
23	PML	chr2:153549376-153550097	GM12878	blood:	n/a	n/a
24	SPI1	chr2:153549619-153549899	GM12891	blood:	n/a	chr2:153549639-153549652 chr2:153549641-153549650
25	MTA3	chr2:153549395-153550135	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:153549811..153552361-chr2:153572191..153576736,5	K562	blood:

Variant related genes	Relation type
PRPF40A	TF binding region
ENSG00000196504	Chromatin interaction
ENSG00000177917	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10497113	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10931263	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10931271	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10931279	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1135617	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11674911	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11676069	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11901227	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12475871	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12989903	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12995388	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12999331	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13006652	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13014141	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13017131	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13022436	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13023779	0.92[EUR][1000 genomes]
rs13023975	0.84[EUR][1000 genomes]
rs1370499	0.91[EUR][1000 genomes]
rs16831440	0.84[EUR][1000 genomes]
rs16831456	0.93[EUR][1000 genomes]
rs17328776	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17400456	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17400938	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17400952	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17400980	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2083097	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2346551	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34199006	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34454505	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34469468	0.84[EUR][1000 genomes]
rs34619076	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34775858	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35002744	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35421285	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35754252	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35894330	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35937874	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36107565	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36122595	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3811568	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3811569	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4575677	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6434172	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66492085	0.93[EUR][1000 genomes]
rs66849546	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6728189	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6736003	0.93[EUR][1000 genomes]
rs71417232	0.93[EUR][1000 genomes]
rs71417235	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72871148	0.93[EUR][1000 genomes]
rs7591590	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7598878	0.94[AMR][1000 genomes];0.99[EUR][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	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153508000-153550800	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr2:153509200-153551200	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr2:153518400-153551000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:153518800-153558000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:153523000-153557800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:153523400-153571800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:153525000-153557800	Weak transcription	Lung	lung
8	chr2:153525000-153571800	Weak transcription	Small Intestine	intestine
9	chr2:153532400-153550800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:153533200-153551000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:153533200-153551600	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:153533200-153558000	Weak transcription	Colonic Mucosa	Colon
13	chr2:153533400-153557800	Weak transcription	Fetal Stomach	stomach
14	chr2:153533400-153558600	Weak transcription	Aorta	Aorta
15	chr2:153533400-153571600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:153533800-153550200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:153533800-153558000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:153533800-153572600	Weak transcription	Fetal Brain Male	brain
19	chr2:153536000-153572600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:153536200-153550200	Weak transcription	NHLF	lung
21	chr2:153537200-153557200	Weak transcription	Thymus	Thymus
22	chr2:153537400-153550600	Weak transcription	Brain Hippocampus Middle	brain
23	chr2:153537400-153565400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:153537600-153550600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:153537600-153557400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:153537600-153558400	Weak transcription	Fetal Brain Female	brain
27	chr2:153537600-153571800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:153537800-153550600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:153537800-153550800	Weak transcription	Brain Substantia Nigra	brain
30	chr2:153537800-153557800	Weak transcription	Brain Germinal Matrix	brain
31	chr2:153538000-153550600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:153538000-153550600	Weak transcription	HSMMtube	muscle
33	chr2:153538400-153550600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr2:153539600-153550000	Weak transcription	Gastric	stomach
35	chr2:153539600-153550600	Weak transcription	Ovary	ovary
36	chr2:153539600-153557800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:153539600-153557800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:153539600-153557800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:153539600-153557800	Weak transcription	Esophagus	oesophagus
40	chr2:153539600-153557800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:153539600-153571800	Weak transcription	Brain Anterior Caudate	brain
42	chr2:153539600-153572400	Weak transcription	Brain Angular Gyrus	brain
43	chr2:153539600-153572400	Weak transcription	Pancreas	Pancrea
44	chr2:153540000-153550600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr2:153540000-153555800	Strong transcription	HepG2	liver
46	chr2:153540400-153552000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:153540600-153550800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr2:153541200-153556600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:153541400-153550000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr2:153542000-153552600	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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