Variant report

Variant	rs1153964
Chromosome Location	chr1:223940382-223940383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr1:223940295-223940841	H1-hESC	embryonic stem cell:	n/a	chr1:223940736-223940746
2	SP1	chr1:223940312-223940856	H1-hESC	embryonic stem cell:	n/a	chr1:223940736-223940746
3	POLR2A	chr1:223938821-223940662	U87	brain:	n/a	n/a
4	POLR2A	chr1:223940306-223940548	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:223940250-223940491	K562	blood:	n/a	n/a
6	E2F6	chr1:223940321-223940846	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:223937857-223950461	K562	blood:	n/a	n/a
8	YY1	chr1:223940353-223940724	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr1:223940096-223941278	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:223939997-223940809	U87	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223888703..223890245-chr1:223939416..223941061,2	K562	blood:
2	chr1:223940335..223944037-chr1:223947483..223951720,4	K562	blood:
3	chr1:223900402..223903093-chr1:223939885..223943104,3	K562	blood:
4	chr1:223937037..223939857-chr1:223940065..223944617,5	K562	blood:
5	chr1:223940271..223942442-chr1:223944013..223946177,2	K562	blood:

No data

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

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1153961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153965	0.89[ASN][1000 genomes]
rs1222078	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222080	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222130	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556780	0.88[AMR][1000 genomes]
rs2298256	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28370070	0.83[ASN][1000 genomes]
rs28370098	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3753048	0.88[ASN][1000 genomes]
rs3754086	0.98[ASN][1000 genomes]
rs6688042	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6704537	0.98[ASN][1000 genomes]
rs7540481	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
7	nsv520609	chr1:223931411-223947081	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv521758	chr1:223931411-223954080	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription 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	36 gene(s)	inside rSNPs	diseases
10	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223931200-223954800	Strong transcription	HMEC	breast
2	chr1:223931400-223954400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:223935800-223952600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:223936600-223954800	Strong transcription	NHEK	skin
5	chr1:223936800-223942800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:223936800-223947400	Weak transcription	Fetal Brain Male	brain
7	chr1:223936800-223954400	Strong transcription	HSMM	muscle
8	chr1:223937000-223940400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:223937000-223940600	Weak transcription	Small Intestine	intestine
10	chr1:223937000-223940800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:223937000-223943200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:223937000-223943400	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr1:223937000-223945400	Strong transcription	Hela-S3	cervix
14	chr1:223937000-223947600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:223937000-223948000	Strong transcription	Lung	lung
16	chr1:223937000-223948200	Weak transcription	Right Atrium	heart
17	chr1:223937000-223951200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:223937000-223954400	Strong transcription	Colonic Mucosa	Colon
19	chr1:223937000-223954400	Strong transcription	Esophagus	oesophagus
20	chr1:223937000-223954400	Strong transcription	Gastric	stomach
21	chr1:223937000-223954800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:223937000-223954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:223937000-223954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:223937000-223954800	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:223937000-223954800	Strong transcription	NHDF-Ad	bronchial
26	chr1:223937000-223954800	Strong transcription	Osteobl	bone
27	chr1:223937000-223957200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:223937000-223959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:223937000-223960000	Weak transcription	Thymus	Thymus
30	chr1:223937200-223940400	Weak transcription	Primary B cells from cord blood	blood
31	chr1:223937200-223940600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:223937200-223942400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:223937200-223943000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:223937200-223948600	Strong transcription	HUVEC	blood vessel
35	chr1:223937200-223951800	Strong transcription	HSMMtube	muscle
36	chr1:223937200-223952600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:223937200-223953000	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:223937200-223954800	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:223937200-223954800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:223937200-223954800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:223937200-223954800	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr1:223937200-223958400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:223937200-223958400	Weak transcription	Fetal Heart	heart
44	chr1:223937400-223941200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:223937400-223942000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:223937400-223942000	Strong transcription	K562	blood
47	chr1:223937400-223943200	Strong transcription	Brain Anterior Caudate	brain
48	chr1:223937400-223943200	Strong transcription	Brain Cingulate Gyrus	brain
49	chr1:223937400-223944200	Strong transcription	Fetal Lung	lung
50	chr1:223937400-223948600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links