Variant report

Variant	rs898877
Chromosome Location	chr1:223930486-223930487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:223930362-223932021	U87	brain:	n/a	n/a
2	JUN	chr1:223930468-223931199	HUVEC	blood vessel:	n/a	chr1:223931017-223931028
3	POLR2A	chr1:223930402-223931907	A549	lung:	n/a	n/a
4	POLR2A	chr1:223930267-223932010	U87	brain:	n/a	n/a
5	POLR2A	chr1:223930437-223930582	K562	blood:	n/a	n/a
6	POLR2A	chr1:223930336-223931274	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr1:223930429-223931020	HUVEC	blood vessel:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223907255..223908800-chr1:223930400..223932243,2	MCF-7	breast:
2	chr1:223929603..223931458-chr1:223939312..223941787,2	K562	blood:
3	chr1:223903418..223905687-chr1:223928822..223931791,2	MCF-7	breast:
4	chr1:223900092..223902158-chr1:223929992..223931627,2	K562	blood:

No data

Variant related genes	Relation type
CAPN2	TF binding region
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10915702	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915707	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915715	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1153965	0.84[EUR][1000 genomes]
rs12066704	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066829	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066831	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069561	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070057	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080250	0.82[EUR][1000 genomes]
rs12088254	0.81[EUR][1000 genomes]
rs1222134	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1222138	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222140	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1222141	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1222142	0.87[EUR][1000 genomes]
rs12562109	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12563291	0.90[EUR][1000 genomes]
rs12563477	0.82[EUR][1000 genomes]
rs12563637	0.93[EUR][1000 genomes]
rs12563713	0.89[EUR][1000 genomes]
rs16842162	0.82[EUR][1000 genomes]
rs17557525	0.80[EUR][1000 genomes]
rs17557623	0.80[EUR][1000 genomes]
rs17597	0.90[EUR][1000 genomes]
rs17598	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17600	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28370026	0.80[EUR][1000 genomes]
rs28370031	0.80[EUR][1000 genomes]
rs28370032	0.80[EUR][1000 genomes]
rs28370043	0.81[EUR][1000 genomes]
rs28370069	0.86[EUR][1000 genomes]
rs28370170	0.82[EUR][1000 genomes]
rs3738373	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738374	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738375	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767716	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3767717	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767718	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59248553	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59275322	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61824003	0.82[EUR][1000 genomes]
rs61824005	0.81[EUR][1000 genomes]
rs6665485	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671245	0.80[EUR][1000 genomes]
rs6674541	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674846	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682412	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6683052	0.80[EUR][1000 genomes]
rs6685475	0.80[EUR][1000 genomes]
rs6693884	0.80[EUR][1000 genomes]
rs7331	0.82[EUR][1000 genomes]
rs751609	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549063	0.80[EUR][1000 genomes]
rs7555226	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs898876	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223915200-223930800	Weak transcription	Primary T cells from cord blood	blood
2	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:223915400-223936200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:223915800-223931600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:223916600-223932600	Weak transcription	Fetal Brain Female	brain
7	chr1:223919200-223935600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:223919200-223936200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:223919800-223931200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:223921200-223932800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr1:223921200-223936000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:223921400-223931400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:223921600-223932800	Weak transcription	Liver	Liver
14	chr1:223921600-223936600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:223921800-223933400	Weak transcription	Brain Angular Gyrus	brain
16	chr1:223921800-223935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:223921800-223936000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:223922200-223934600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:223922200-223935600	Weak transcription	Fetal Brain Male	brain
20	chr1:223922800-223930600	Weak transcription	Spleen	Spleen
21	chr1:223922800-223930800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:223922800-223931600	Weak transcription	Brain Germinal Matrix	brain
23	chr1:223922800-223934800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:223923000-223931800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:223925200-223934600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:223925400-223930600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:223925400-223930800	Weak transcription	Gastric	stomach
28	chr1:223925400-223931800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:223925400-223931800	Weak transcription	Ovary	ovary
30	chr1:223925400-223934800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:223926800-223930600	Weak transcription	Pancreas	Pancrea
32	chr1:223926800-223930800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:223926800-223931400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:223926800-223931600	Weak transcription	Hela-S3	cervix
35	chr1:223926800-223932800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:223927400-223933000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:223927600-223931600	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:223927800-223930600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:223927800-223930600	Weak transcription	Fetal Lung	lung
40	chr1:223927800-223931000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:223927800-223931600	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:223927800-223935400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:223928000-223930600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:223928000-223930600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:223928000-223930600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:223928000-223930600	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:223928000-223930600	Weak transcription	Right Ventricle	heart
48	chr1:223928000-223930600	Weak transcription	HSMMtube	muscle
49	chr1:223928000-223930600	Weak transcription	NHDF-Ad	bronchial
50	chr1:223928000-223930600	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links