Variant report

Variant	rs13228358
Chromosome Location	chr7:124568467-124568468
allele	C/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	chr7:124566718-124570402	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:124568199..124570049-chr7:127030538..127032262,2	K562	blood:
2	chr7:124521370..124523136-chr7:124567552..124569550,2	K562	blood:
3	chr7:124534351..124537236-chr7:124567413..124569702,2	K562	blood:

Variant related genes	Relation type
POT1-AS1	TF binding region
ENSG00000048405	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10230948	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10234698	0.84[ASN][1000 genomes]
rs10241745	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10268290	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10280030	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10281773	0.81[EUR][1000 genomes]
rs1034794	0.83[ASN][1000 genomes]
rs1034795	0.83[ASN][1000 genomes]
rs11766412	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11767519	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11768553	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11770818	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11772420	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11972411	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11978268	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12532038	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12533661	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12534967	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12534983	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12537983	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12538061	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12539481	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12706625	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12706627	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13222197	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13240050	0.81[EUR][1000 genomes]
rs1481334	0.81[EUR][1000 genomes]
rs1541417	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17147465	0.84[ASN][1000 genomes]
rs17147723	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2101100	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127968	0.88[EUR][1000 genomes]
rs2127969	0.87[EUR][1000 genomes]
rs2127970	0.88[EUR][1000 genomes]
rs2291207	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2402754	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2402761	0.86[EUR][1000 genomes]
rs28820412	0.87[EUR][1000 genomes]
rs33964002	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34326887	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35146319	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35423300	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35550222	0.82[ASN][1000 genomes]
rs4141073	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4360236	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4501522	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4728007	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4731210	0.85[ASN][1000 genomes]
rs60678110	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62480260	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62480274	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6466951	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6466959	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6943703	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6943797	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6945563	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6946962	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6963885	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6968018	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs716991	0.85[ASN][1000 genomes]
rs719974	0.81[EUR][1000 genomes]
rs727521	0.81[EUR][1000 genomes]
rs7782296	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7782351	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7784168	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7784285	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7786989	0.87[EUR][1000 genomes]
rs7787570	0.86[EUR][1000 genomes]
rs7787804	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7794637	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7795610	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7796751	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7801755	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7804052	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7806890	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9656320	0.83[EUR][1000 genomes];0.85[ASN][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	nsv429809	chr7:123937674-124835925	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	esv3446198	chr7:124358002-124586856	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv889135	chr7:124462081-124584834	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv464707	chr7:124486980-124572288	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv608341	chr7:124486980-124572288	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv889137	chr7:124513770-124584834	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv889138	chr7:124518766-124584834	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv608342	chr7:124549573-124600505	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:124498200-124568800	Weak transcription	Brain Anterior Caudate	brain
2	chr7:124527600-124569000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:124527600-124569000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr7:124530000-124569000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr7:124532000-124569000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr7:124532600-124568800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr7:124532600-124569000	Weak transcription	HSMM	muscle
8	chr7:124532800-124569000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr7:124538000-124569200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr7:124541000-124568600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:124541000-124569000	Weak transcription	Fetal Muscle Leg	muscle
12	chr7:124541400-124568800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:124541400-124568800	Weak transcription	Fetal Intestine Small	intestine
14	chr7:124541400-124569000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:124541400-124569000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:124541400-124569000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:124541400-124569400	Weak transcription	Lung	lung
18	chr7:124541600-124569200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr7:124548400-124569000	Weak transcription	NH-A	brain
20	chr7:124550200-124569200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr7:124550600-124568800	Weak transcription	Fetal Intestine Large	intestine
22	chr7:124550800-124569000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr7:124551000-124569000	Weak transcription	HSMMtube	muscle
24	chr7:124551400-124568800	Weak transcription	Fetal Kidney	kidney
25	chr7:124551800-124568800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr7:124552400-124569000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr7:124553200-124568800	Weak transcription	Fetal Thymus	thymus
28	chr7:124553400-124568800	Weak transcription	HMEC	breast
29	chr7:124554600-124568600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:124555400-124569000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr7:124555600-124568800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr7:124555600-124569000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr7:124555800-124568800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr7:124557200-124568800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr7:124557400-124569000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr7:124558200-124568800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr7:124558200-124568800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr7:124558200-124569200	Weak transcription	Left Ventricle	heart
39	chr7:124560000-124569400	Weak transcription	Small Intestine	intestine
40	chr7:124560600-124569000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr7:124562800-124568800	Weak transcription	A549	lung
42	chr7:124563400-124570200	Active TSS	GM12878-XiMat	blood
43	chr7:124563800-124568800	Weak transcription	Osteobl	bone
44	chr7:124564800-124568600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr7:124565000-124568800	Weak transcription	Hela-S3	cervix
46	chr7:124565200-124568800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr7:124565600-124568600	Strong transcription	Primary B cells from cord blood	blood
48	chr7:124565600-124568800	Weak transcription	NHEK	skin
49	chr7:124566200-124568800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr7:124566200-124568800	Weak 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