Variant report

Variant	rs2917781
Chromosome Location	chr2:55510569-55510570
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55508730-55510913	HepG2	liver:	n/a	n/a
2	FOXA1	chr2:55510281-55510672	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:55510379-55510902	HepG2	liver:	n/a	n/a
4	USF1	chr2:55510541-55510965	K562	blood:	n/a	n/a
5	POLR2A	chr2:55509081-55511652	K562	blood:	n/a	n/a
6	FOXA2	chr2:55510360-55510683	HepG2	liver:	n/a	n/a
7	SRF	chr2:55510383-55510578	HepG2	liver:	n/a	chr2:55510543-55510558 chr2:55510542-55510560
8	POLR2A	chr2:55510365-55510822	K562	blood:	n/a	n/a
9	POLR2A	chr2:55508889-55510729	PANC-1	pancreas:	n/a	n/a
10	GTF3C2	chr2:55508654-55510760	K562	blood:	n/a	n/a
11	MYC	chr2:55510422-55510949	K562	blood:	n/a	chr2:55510778-55510788
12	JUND	chr2:55510520-55510631	K562	blood:	n/a	n/a
13	TBP	chr2:55510438-55510788	K562	blood:	n/a	n/a
14	POLR2A	chr2:55508876-55510718	K562	blood:	n/a	n/a
15	POLR2A	chr2:55510519-55511096	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55494750..55497639-chr2:55510154..55512422,2	MCF-7	breast:
2	chr2:55508571..55512777-chr2:55645734..55648780,3	K562	blood:
3	chr2:55508376..55510742-chr2:55843787..55846796,4	K562	blood:
4	chr2:55494928..55498059-chr2:55506695..55512310,8	K562	blood:
5	chr2:55509373..55510992-chr2:55512785..55514521,3	MCF-7	breast:
6	chr2:55491409..55498987-chr2:55507178..55511380,11	MCF-7	breast:
7	chr2:55507859..55511177-chr2:55645007..55647398,3	K562	blood:
8	chr2:55458112..55461105-chr2:55507986..55510921,3	MCF-7	breast:
9	chr2:55508669..55511212-chr2:55645960..55648569,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000206964	TF binding region
ENSG00000085760	Chromatin interaction
ENSG00000143947	Chromatin interaction
ENSG00000115355	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000206964	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10209598	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10496041	0.88[ASN][1000 genomes]
rs11125562	0.94[ASN][1000 genomes]
rs11125563	0.83[AFR][1000 genomes]
rs11884753	0.90[AFR][1000 genomes]
rs11892007	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11904107	0.94[ASN][1000 genomes]
rs12104902	0.94[ASN][1000 genomes]
rs12105322	0.94[ASN][1000 genomes]
rs12105731	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12617316	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13016664	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13031346	0.85[ASN][1000 genomes]
rs13407931	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1437387	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1437388	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1545120	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1545121	0.83[AFR][1000 genomes]
rs17046834	0.98[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2249856	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576691	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576692	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576693	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576694	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576697	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2576698	0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2576702	0.94[ASN][1000 genomes]
rs2589058	0.95[AFR][1000 genomes]
rs2589060	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2589061	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2589063	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2589067	0.80[ASN][1000 genomes]
rs2589110	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2589111	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2589112	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2589113	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2589114	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2589115	0.80[ASN][1000 genomes]
rs2589116	0.94[ASN][1000 genomes]
rs2589117	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2917775	0.89[AFR][1000 genomes]
rs2920959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920972	0.94[ASN][1000 genomes]
rs2920973	0.84[AFR][1000 genomes]
rs2966465	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57105158	0.94[ASN][1000 genomes]
rs59554860	0.88[ASN][1000 genomes]
rs6545484	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6705991	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6718747	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6721211	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6726732	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6733567	0.94[ASN][1000 genomes]
rs6738970	0.87[AFR][1000 genomes]
rs6739348	0.87[AFR][1000 genomes]
rs6740631	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6746287	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs73939905	0.94[ASN][1000 genomes]
rs9784090	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv1799450	chr2:55494904-55520842	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55501000-55517000	Weak transcription	Hela-S3	cervix
2	chr2:55508000-55510600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:55508800-55510600	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr2:55508800-55510600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:55508800-55510600	Active TSS	A549	lung
6	chr2:55508800-55510800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:55508800-55510800	Active TSS	Rectal Smooth Muscle	rectum
8	chr2:55508800-55511000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:55508800-55511000	Active TSS	Right Atrium	heart
10	chr2:55508800-55511400	Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr2:55509000-55510600	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr2:55509000-55510600	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr2:55509000-55510600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:55509000-55510600	Active TSS	K562	blood
15	chr2:55509000-55541200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:55509200-55510600	Active TSS	Pancreas	Pancrea
17	chr2:55509200-55511000	Active TSS	Stomach Smooth Muscle	stomach
18	chr2:55509400-55515600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:55509400-55545200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr2:55509600-55510600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:55509600-55510600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:55509600-55511000	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr2:55509600-55511200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:55509600-55522600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:55509800-55510600	Weak transcription	Small Intestine	intestine
26	chr2:55509800-55514600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:55509800-55518600	Weak transcription	HMEC	breast
28	chr2:55509800-55521800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:55510000-55510600	Enhancers	Fetal Thymus	thymus
30	chr2:55510000-55510600	Enhancers	Lung	lung
31	chr2:55510000-55510600	Flanking Active TSS	HepG2	liver
32	chr2:55510000-55510800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:55510000-55511000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:55510000-55511000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr2:55510000-55511000	Enhancers	Spleen	Spleen
36	chr2:55510000-55511200	Enhancers	Primary B cells from peripheral blood	blood
37	chr2:55510000-55511200	Enhancers	Fetal Heart	heart
38	chr2:55510000-55511800	Weak transcription	Gastric	stomach
39	chr2:55510000-55512600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:55510000-55513600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:55510000-55514400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:55510000-55515400	Weak transcription	Brain Substantia Nigra	brain
43	chr2:55510000-55516200	Weak transcription	Fetal Lung	lung
44	chr2:55510000-55518800	Weak transcription	Brain Angular Gyrus	brain
45	chr2:55510000-55521600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:55510000-55521600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:55510000-55521800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:55510000-55521800	Weak transcription	Fetal Brain Male	brain
49	chr2:55510000-55521800	Weak transcription	NHEK	skin
50	chr2:55510000-55522000	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links