Variant report

Variant	rs1222148
Chromosome Location	chr1:223956664-223956665
allele	C/G
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	chr1:223956590-223957719	K562	blood:	n/a	n/a
2	POLR2A	chr1:223956584-223956991	K562	blood:	n/a	n/a
3	POLR2A	chr1:223956518-223969626	K562	blood:	n/a	n/a
4	POLR2A	chr1:223956580-223956871	K562	blood:	n/a	n/a

Variant related genes	Relation type
CAPN2	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1003061	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1153928	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1153937	0.93[ASN][1000 genomes]
rs1153938	0.92[ASN][1000 genomes]
rs1153943	0.89[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs1153944	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1153946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153950	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153954	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]
rs1153956	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1222081	1.00[CEU][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1222123	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222126	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1222127	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1222147	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222153	0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1222158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1228475	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1538140	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17739	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982611	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60739082	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6604726	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6658724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6661816	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6667215	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6694471	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6698919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs898878	0.89[AMR][1000 genomes];0.92[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	chr1:223937000-223957200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:223937000-223959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:223937000-223960000	Weak transcription	Thymus	Thymus
4	chr1:223937200-223958400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:223937200-223958400	Weak transcription	Fetal Heart	heart
6	chr1:223941000-223957600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:223941000-223958200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:223941000-223959400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:223941200-223961600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:223942400-223958800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:223947000-223957200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:223948000-223957600	Weak transcription	Fetal Brain Male	brain
13	chr1:223948400-223957200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:223949600-223958400	Weak transcription	Small Intestine	intestine
15	chr1:223950000-223957600	Weak transcription	Right Atrium	heart
16	chr1:223950200-223957000	Weak transcription	Psoas Muscle	Psoas
17	chr1:223951400-223957200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:223952000-223956800	Weak transcription	Liver	Liver
19	chr1:223952000-223957200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:223953200-223956800	Weak transcription	Placenta	Placenta
21	chr1:223953600-223956800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:223953600-223956800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:223953800-223956800	Weak transcription	Aorta	Aorta
24	chr1:223953800-223956800	Weak transcription	Fetal Intestine Large	intestine
25	chr1:223954000-223956800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:223954000-223957200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:223954200-223956800	Weak transcription	HUVEC	blood vessel
28	chr1:223954200-223957200	Weak transcription	Brain Angular Gyrus	brain
29	chr1:223954200-223957200	Weak transcription	Brain Germinal Matrix	brain
30	chr1:223954200-223957200	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:223954200-223957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:223954200-223958800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:223954400-223956800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:223954400-223956800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:223954400-223956800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:223954400-223956800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:223954400-223956800	Weak transcription	Esophagus	oesophagus
38	chr1:223954400-223956800	Weak transcription	NHLF	lung
39	chr1:223954400-223957000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:223954400-223957000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr1:223954400-223957000	Weak transcription	Left Ventricle	heart
42	chr1:223954400-223957000	Weak transcription	Pancreas	Pancrea
43	chr1:223954400-223957200	Weak transcription	Brain Substantia Nigra	brain
44	chr1:223954400-223957200	Weak transcription	Spleen	Spleen
45	chr1:223954400-223957200	Weak transcription	Hela-S3	cervix
46	chr1:223954400-223957200	Weak transcription	HSMMtube	muscle
47	chr1:223954400-223958600	Weak transcription	Ovary	ovary
48	chr1:223954400-223961800	Weak transcription	HepG2	liver
49	chr1:223954800-223956800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:223954800-223956800	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links