Variant report

Variant	rs13223142
Chromosome Location	chr7:64382270-64382271
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:64363939..64365901-chr7:64381813..64383330,2	K562	blood:
2	chr7:64371294..64373665-chr7:64381252..64383670,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 40 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11773228	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11773456	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12532791	0.81[AMR][1000 genomes]
rs13225933	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13236444	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13236784	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1830007	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1966140	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2017252	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34238742	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35058955	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35065007	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3813700	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829003	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4644117	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4717222	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4718154	0.82[AMR][1000 genomes]
rs4718156	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4718169	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4718170	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56063644	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62455121	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62458435	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6460209	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6953002	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6957266	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6965861	0.81[AMR][1000 genomes]
rs7776640	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7782713	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7786519	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7796024	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7796284	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7797115	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7798063	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7798465	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7805817	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9638209	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422405	chr7:63709739-64632341	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv427787	chr7:63741770-64419520	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv464518	chr7:63881238-64506904	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv607312	chr7:63881238-64506904	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv888275	chr7:63990100-64468590	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv888276	chr7:63990100-64511564	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv1022042	chr7:64226499-64566945	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv1026390	chr7:64240323-64414364	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv1033291	chr7:64273434-64406276	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv508457	chr7:64286522-64391112	Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
11	nsv888282	chr7:64299645-64511564	Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	esv3506582	chr7:64323055-64563984	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	esv3506583	chr7:64323055-64563984	Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv1019180	chr7:64329889-64512842	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
15	nsv888283	chr7:64343985-64511564	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
16	esv2752165	chr7:64345822-65208605	Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
17	nsv981497	chr7:64366868-64385550	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:40)

SNP	Gene	Cis/trans	Tissue	Source
rs13223142	ZNF273	cis	Heart Left Ventricle	GTEx
rs13223142	ZNF273	cis	lung	GTEx
rs13223142	RP11-797H7.5	cis	Artery Tibial	GTEx
rs13223142	ZNF273	cis	Thyroid	GTEx
rs13223142	RP11-797H7.3	cis	Whole Blood	GTEx
rs13223142	RP11-797H7.5	cis	Stomach	GTEx
rs13223142	RP11-797H7.3	cis	Thyroid	GTEx
rs13223142	RP11-460N20.5	cis	Thyroid	GTEx
rs13223142	SEPHS1P1	cis	Esophagus Muscularis	GTEx
rs13223142	RP11-797H7.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13223142	RP11-797H7.5	cis	Nerve Tibial	GTEx
rs13223142	RP11-797H7.3	cis	Artery Aorta	GTEx
rs13223142	SEPHS1P1	cis	Thyroid	GTEx
rs13223142	CCT6P3	cis	Esophagus Mucosa	GTEx
rs13223142	RP11-797H7.3	cis	Nerve Tibial	GTEx
rs13223142	RP11-797H7.3	cis	Adipose Subcutaneous	GTEx
rs13223142	RP11-797H7.3	cis	Muscle Skeletal	GTEx
rs13223142	RP11-797H7.3	cis	Artery Tibial	GTEx
rs13223142	INTS4L1	cis	Skin Sun Exposed Lower leg	GTEx
rs13223142	SEPHS1P1	cis	Nerve Tibial	GTEx
rs13223142	RP11-797H7.5	cis	Skin Sun Exposed Lower leg	GTEx
rs13223142	RP11-797H7.5	cis	Heart Left Ventricle	GTEx
rs13223142	RP11-797H7.3	cis	lung	GTEx
rs13223142	RP11-797H7.5	cis	lung	GTEx
rs13223142	RP11-797H7.3	cis	Esophagus Muscularis	GTEx
rs13223142	RP11-460N20.5	cis	Whole Blood	GTEx
rs13223142	SEPHS1P1	cis	Skin Sun Exposed Lower leg	GTEx
rs13223142	SEPHS1P1	cis	Artery Tibial	GTEx
rs13223142	RP11-797H7.3	cis	Esophagus Mucosa	GTEx
rs13223142	RP11-460N20.4	cis	Adipose Subcutaneous	GTEx
rs13223142	CCT6P3	cis	Skin Sun Exposed Lower leg	GTEx
rs13223142	RP11-460N20.5	cis	Adipose Subcutaneous	GTEx
rs13223142	RP11-460N20.5	cis	Nerve Tibial	GTEx
rs13223142	RP11-667F9.1	cis	Nerve Tibial	GTEx
rs13223142	RP11-797H7.5	cis	Adipose Subcutaneous	GTEx
rs13223142	RP11-667F9.1	cis	Adipose Subcutaneous	GTEx
rs13223142	RP11-797H7.3	cis	Stomach	GTEx
rs13223142	RP11-797H7.5	cis	Esophagus Muscularis	GTEx
rs13223142	RP11-797H7.5	cis	Thyroid	GTEx
rs13223142	RP11-797H7.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64364400-64382600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:64364600-64383200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:64364600-64386400	Weak transcription	HUVEC	blood vessel
4	chr7:64364600-64387200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:64367800-64392600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:64368000-64390200	ZNF genes & repeats	Dnd41	blood
7	chr7:64368600-64383400	Weak transcription	Osteobl	bone
8	chr7:64369000-64382600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr7:64369000-64387200	Weak transcription	Left Ventricle	heart
10	chr7:64369600-64387400	Weak transcription	Pancreas	Pancrea
11	chr7:64369800-64386000	Weak transcription	Psoas Muscle	Psoas
12	chr7:64369800-64390400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:64371800-64390000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
14	chr7:64372200-64392600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:64372600-64384800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr7:64374200-64383200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr7:64374400-64387600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:64375200-64384800	Weak transcription	Stomach Mucosa	stomach
19	chr7:64375200-64389200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr7:64375200-64390000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr7:64375400-64385200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:64375600-64382800	Weak transcription	Small Intestine	intestine
23	chr7:64375600-64385600	Weak transcription	Colon Smooth Muscle	Colon
24	chr7:64376000-64385400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:64376000-64386200	Weak transcription	Brain Hippocampus Middle	brain
26	chr7:64376200-64383600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr7:64376200-64383800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr7:64376600-64388000	Weak transcription	Brain Anterior Caudate	brain
29	chr7:64376600-64389200	Weak transcription	Right Ventricle	heart
30	chr7:64376800-64389200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:64377000-64383000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:64377000-64383000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr7:64377000-64388800	ZNF genes & repeats	GM12878-XiMat	blood
34	chr7:64377600-64389400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
35	chr7:64377600-64389600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr7:64377800-64382400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr7:64377800-64382600	Weak transcription	Fetal Brain Male	brain
38	chr7:64378000-64383000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr7:64378000-64400800	Weak transcription	Brain Angular Gyrus	brain
40	chr7:64378200-64383000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr7:64378200-64387200	Weak transcription	Fetal Heart	heart
42	chr7:64378200-64387800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
43	chr7:64378200-64389200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
44	chr7:64378600-64383000	Weak transcription	Fetal Kidney	kidney
45	chr7:64378600-64385200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr7:64378600-64385600	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr7:64378600-64389400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr7:64378800-64383200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr7:64378800-64389000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr7:64379000-64387200	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links