Variant report

Variant	rs12123975
Chromosome Location	chr1:152004804-152004805
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	chr1:152004043..152013121-chr1:152013584..152022966,19	K562	blood:
2	chr1:152003508..152006016-chr3:64240085..64241940,2	MCF-7	breast:
3	chr1:151958520..151979218-chr1:151992734..152014750,97	MCF-7	breast:
4	chr1:151997592..152000078-chr1:152004564..152007278,3	K562	blood:
5	chr1:151904319..151906408-chr1:152003368..152007237,3	MCF-7	breast:
6	chr1:152003216..152005599-chr1:152046745..152048519,2	MCF-7	breast:
7	chr1:152004094..152009269-chr1:152022985..152027910,7	K562	blood:
8	chr1:151978047..151980074-chr1:152004028..152006807,2	K562	blood:
9	chr1:152003076..152005594-chr1:152022985..152024993,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000229021	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000197747	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11803731	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12082156	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130862	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12134184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17646946	1.00[CHB][hapmap]
rs2999547	0.91[TSI][hapmap]
rs2999550	0.80[EUR][1000 genomes]
rs3007671	0.87[TSI][hapmap]
rs34974291	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36010924	1.00[ASN][1000 genomes]
rs4845418	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs71625168	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12123975	LCE3E	cis	parietal	SCAN
rs12123975	KCNK5	trans	cerebellum	SCAN
rs12123975	S100A8	cis	parietal	SCAN
rs12123975	PSMB4	cis	cerebellum	SCAN
rs12123975	SELENBP1	cis	cerebellum	SCAN
rs12123975	LCE2C	cis	cerebellum	SCAN
rs12123975	LELP1	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151986800-152007400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:151997000-152006600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:151997000-152007000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:152000200-152005000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:152001600-152005000	Strong transcription	Primary T cells from cord blood	blood
6	chr1:152001600-152006000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
7	chr1:152001800-152005000	Weak transcription	Right Ventricle	heart
8	chr1:152001800-152007200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:152002000-152007400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:152002400-152005200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:152002600-152005000	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr1:152002600-152005400	Strong transcription	A549	lung
13	chr1:152002600-152005600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:152002600-152005800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr1:152002600-152005800	Strong transcription	Fetal Thymus	thymus
16	chr1:152002600-152006400	Strong transcription	Fetal Muscle Leg	muscle
17	chr1:152002800-152005200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:152002800-152006200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:152002800-152006800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:152003000-152005400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:152003000-152005400	Strong transcription	Placenta	Placenta
22	chr1:152003000-152006000	Strong transcription	Fetal Intestine Small	intestine
23	chr1:152003000-152006400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:152003200-152005200	Genic enhancers	Monocytes-CD14+_RO01746	blood
25	chr1:152003200-152005400	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr1:152003200-152005400	Strong transcription	Left Ventricle	heart
27	chr1:152003200-152005600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:152003200-152005600	Strong transcription	Adipose Nuclei	Adipose
29	chr1:152003200-152005600	Strong transcription	Thymus	Thymus
30	chr1:152003200-152006000	Strong transcription	HUVEC	blood vessel
31	chr1:152003200-152006200	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr1:152003200-152006400	Genic enhancers	Primary monocytes fromperipheralblood	blood
33	chr1:152003200-152006400	Strong transcription	HSMMtube	muscle
34	chr1:152003200-152006600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:152003400-152005200	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr1:152003400-152005400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:152003400-152005800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:152003400-152006000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:152003400-152006000	Strong transcription	Osteobl	bone
40	chr1:152003400-152006200	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:152003400-152006400	Strong transcription	Fetal Intestine Large	intestine
42	chr1:152003400-152006400	Strong transcription	Lung	lung
43	chr1:152003400-152006400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr1:152003400-152006400	Strong transcription	NH-A	brain
45	chr1:152003400-152006800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:152003600-152006400	Strong transcription	Fetal Muscle Trunk	muscle
47	chr1:152003600-152006600	Strong transcription	Fetal Stomach	stomach
48	chr1:152003800-152005400	Genic enhancers	NHEK	skin
49	chr1:152003800-152005600	Strong transcription	Hela-S3	cervix
50	chr1:152003800-152006400	Strong transcription	HSMM	muscle

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