Variant report

Variant	rs1153954
Chromosome Location	chr1:223957335-223957336
allele	A/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	chr1:223957197-223957511	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:223957114-223958466	U87	brain:	n/a	n/a
3	POLR2A	chr1:223956590-223957719	K562	blood:	n/a	n/a
4	STAT3	chr1:223957179-223957379	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:223956518-223969626	K562	blood:	n/a	n/a
6	POLR2A	chr1:223957232-223957871	K562	blood:	n/a	n/a
7	POLR2A	chr1:223957277-223958402	U87	brain:	n/a	n/a
8	POLR2A	chr1:223956762-223960838	A549	lung:	n/a	n/a
9	POLR2A	chr1:223957290-223957691	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:223957191-223958448	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223898558..223902080-chr1:223957242..223958839,3	K562	blood:
2	chr1:223888744..223890349-chr1:223956680..223958231,2	MCF-7	breast:

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

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1003061	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1153928	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1153937	0.93[ASN][1000 genomes]
rs1153938	0.92[ASN][1000 genomes]
rs1153943	0.84[CHB][hapmap];0.93[ASN][1000 genomes]
rs1153944	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1153946	0.91[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153950	0.82[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153952	0.91[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153956	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1222081	0.91[CEU][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1222123	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222126	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1222127	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1222147	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222148	0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222153	0.89[CHB][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1222158	0.91[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1228475	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1538140	0.91[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17739	0.91[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982611	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60739082	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6604726	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6658724	0.91[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6661816	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6667215	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6675712	0.83[JPT][hapmap]
rs6694471	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6698919	0.91[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs898878	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
8	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:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223937000-223959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:223937000-223960000	Weak transcription	Thymus	Thymus
3	chr1:223937200-223958400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:223937200-223958400	Weak transcription	Fetal Heart	heart
5	chr1:223941000-223957600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:223941000-223958200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:223941000-223959400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:223941200-223961600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:223942400-223958800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:223948000-223957600	Weak transcription	Fetal Brain Male	brain
11	chr1:223949600-223958400	Weak transcription	Small Intestine	intestine
12	chr1:223950000-223957600	Weak transcription	Right Atrium	heart
13	chr1:223954200-223957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:223954200-223958800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:223954400-223958600	Weak transcription	Ovary	ovary
16	chr1:223954400-223961800	Weak transcription	HepG2	liver
17	chr1:223954800-223964000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:223956400-223957400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:223956400-223958400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:223956600-223957400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:223956600-223957400	Strong transcription	K562	blood
22	chr1:223956600-223957600	Strong transcription	Osteobl	bone
23	chr1:223956600-223957800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:223956600-223957800	ZNF genes & repeats	Fetal Thymus	thymus
25	chr1:223956600-223957800	Strong transcription	A549	lung
26	chr1:223956600-223958000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:223956600-223958000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:223956600-223958000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:223956600-223958000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:223956600-223958000	Strong transcription	NH-A	brain
31	chr1:223956600-223958200	Strong transcription	Fetal Intestine Small	intestine
32	chr1:223956600-223958200	Strong transcription	Stomach Mucosa	stomach
33	chr1:223956600-223958400	Strong transcription	Gastric	stomach
34	chr1:223956600-223958400	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:223956600-223958600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:223956600-223958600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:223956600-223958600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:223956600-223958600	Strong transcription	Colon Smooth Muscle	Colon
39	chr1:223956600-223958600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr1:223956600-223958600	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr1:223956600-223958600	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:223956600-223958600	Strong transcription	Stomach Smooth Muscle	stomach
43	chr1:223956600-223958600	Strong transcription	HMEC	breast
44	chr1:223956600-223958800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:223956600-223958800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:223956600-223958800	Weak transcription	Primary B cells from cord blood	blood
47	chr1:223956600-223958800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr1:223956600-223958800	Strong transcription	Fetal Muscle Leg	muscle
49	chr1:223956600-223959000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:223956600-223959000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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