Variant report

Variant	rs28370043
Chromosome Location	chr1:223915921-223915922
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223898332..223906168-chr1:223910455..223917097,17	K562	blood:
2	chr1:223913291..223915988-chr1:223981454..223983055,2	K562	blood:
3	chr1:223899168..223900850-chr1:223913497..223916272,3	MCF-7	breast:
4	chr1:223914562..223916498-chr1:223920143..223922062,2	K562	blood:
5	chr1:223914702..223917591-chr1:223920131..223923452,6	K562	blood:
6	chr1:223915826..223918177-chr1:223937169..223939533,2	K562	blood:
7	chr1:223889048..223892009-chr1:223912186..223915983,3	K562	blood:
8	chr1:223893369..223895448-chr1:223913219..223916092,2	K562	blood:
9	chr1:223915458..223917268-chr1:223983220..223985894,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10465524	1.00[ASN][1000 genomes]
rs10495215	0.82[EUR][1000 genomes]
rs10495216	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10495217	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10915702	0.83[EUR][1000 genomes]
rs10915707	0.80[EUR][1000 genomes]
rs1153958	0.87[ASN][1000 genomes]
rs12066704	0.83[EUR][1000 genomes]
rs12066829	0.83[EUR][1000 genomes]
rs12066831	0.83[EUR][1000 genomes]
rs12069561	0.80[EUR][1000 genomes]
rs12070057	0.83[EUR][1000 genomes]
rs1222134	0.80[EUR][1000 genomes]
rs1222138	0.84[EUR][1000 genomes]
rs1222140	0.85[EUR][1000 genomes]
rs1222141	0.85[EUR][1000 genomes]
rs1222142	0.84[EUR][1000 genomes]
rs12562109	0.80[EUR][1000 genomes]
rs12563291	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12563477	1.00[ASN][1000 genomes]
rs12563637	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12563713	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17557288	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17557525	0.99[EUR][1000 genomes]
rs17557623	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17597	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17598	0.80[EUR][1000 genomes]
rs17600	0.80[EUR][1000 genomes]
rs28370026	0.99[EUR][1000 genomes]
rs28370031	0.99[EUR][1000 genomes]
rs28370032	0.99[EUR][1000 genomes]
rs28370069	0.81[EUR][1000 genomes]
rs28370073	1.00[ASN][1000 genomes]
rs28370074	1.00[ASN][1000 genomes]
rs28370088	1.00[ASN][1000 genomes]
rs3738373	0.80[EUR][1000 genomes]
rs3738374	0.80[EUR][1000 genomes]
rs3738375	0.80[EUR][1000 genomes]
rs3767716	0.81[EUR][1000 genomes]
rs3767717	0.80[EUR][1000 genomes]
rs3767718	0.80[EUR][1000 genomes]
rs59248553	0.83[EUR][1000 genomes]
rs59275322	0.85[EUR][1000 genomes]
rs61823964	0.82[EUR][1000 genomes]
rs61823979	0.96[EUR][1000 genomes]
rs6665485	0.81[EUR][1000 genomes]
rs6671245	0.99[EUR][1000 genomes]
rs6683052	0.99[EUR][1000 genomes]
rs6685475	0.99[EUR][1000 genomes]
rs6693372	0.96[EUR][1000 genomes]
rs6693884	0.99[EUR][1000 genomes]
rs6696053	1.00[ASN][1000 genomes]
rs751609	0.83[EUR][1000 genomes]
rs7548911	0.87[ASN][1000 genomes]
rs7549063	0.99[EUR][1000 genomes]
rs7555226	0.85[EUR][1000 genomes]
rs898876	0.83[EUR][1000 genomes]
rs898877	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv873213	chr1:223885843-223924236	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28370043	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223903600-223922400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:223904400-223922400	Genic enhancers	NHLF	lung
3	chr1:223906600-223921000	Weak transcription	Fetal Brain Male	brain
4	chr1:223910800-223916400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:223910800-223916800	Genic enhancers	Gastric	stomach
6	chr1:223910800-223919800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:223911800-223917200	Genic enhancers	Muscle Satellite Cultured Cells	--
8	chr1:223912600-223916000	Genic enhancers	Rectal Mucosa Donor 29	rectum
9	chr1:223913000-223916600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:223913200-223916000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:223913200-223916200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:223913200-223916200	Enhancers	Left Ventricle	heart
13	chr1:223913400-223916000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:223913400-223916000	Enhancers	Right Atrium	heart
15	chr1:223913400-223916400	Enhancers	Placenta Amnion	Placenta Amnion
16	chr1:223913400-223916400	Enhancers	Spleen	Spleen
17	chr1:223913600-223916000	Enhancers	Right Ventricle	heart
18	chr1:223913800-223916600	Enhancers	Fetal Thymus	thymus
19	chr1:223914400-223916000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:223914400-223916200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:223914400-223916400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:223914400-223917800	Weak transcription	Brain Angular Gyrus	brain
23	chr1:223914400-223921800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:223914600-223916600	Strong transcription	Fetal Brain Female	brain
25	chr1:223914600-223916800	Genic enhancers	NHDF-Ad	bronchial
26	chr1:223914600-223918400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:223914800-223916800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:223914800-223916800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:223914800-223919000	Weak transcription	Brain Germinal Matrix	brain
30	chr1:223915000-223916000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
31	chr1:223915000-223916000	Genic enhancers	Rectal Mucosa Donor 31	rectum
32	chr1:223915000-223916600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:223915000-223917600	Strong transcription	Fetal Intestine Small	intestine
34	chr1:223915000-223919800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:223915000-223920800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:223915000-223920800	Weak transcription	Liver	Liver
37	chr1:223915000-223921000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:223915000-223921000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:223915000-223921000	Genic enhancers	NHEK	skin
40	chr1:223915200-223916000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
41	chr1:223915200-223916600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr1:223915200-223918400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr1:223915200-223918400	Weak transcription	Fetal Heart	heart
44	chr1:223915200-223918400	Weak transcription	Small Intestine	intestine
45	chr1:223915200-223918600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:223915200-223919000	Weak transcription	Psoas Muscle	Psoas
47	chr1:223915200-223930800	Weak transcription	Primary T cells from cord blood	blood
48	chr1:223915400-223916000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:223915400-223916200	Genic enhancers	Esophagus	oesophagus
50	chr1:223915400-223916600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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