Variant report

Variant	rs12129158
Chromosome Location	chr1:75597376-75597377
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	CTBP2	chr1:75595360-75597561	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:75597361-75597423	Gliobla	brain:	n/a	n/a
3	SUZ12	chr1:75595125-75598694	H1-hESC	embryonic stem cell:	n/a	n/a
4	SUZ12	chr1:75594519-75601637	NT2-D1	testis:	n/a	n/a
5	POLR2A	chr1:75596570-75599860	H1-neurons	neurons:	n/a	n/a
6	SIN3A	chr1:75595809-75597416	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:75596503-75602546	H1-neurons	neurons:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC44A5-1	chr1:75595659-75597638	ENSG00000224149.1

Variant related genes	Relation type
LHX8	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12129029	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129193	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133614	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138223	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142460	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12723906	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726443	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12729173	1.00[ASN][1000 genomes]
rs12732329	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12741928	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12751207	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526502	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526510	1.00[ASN][1000 genomes]
rs1526511	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1852348	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1852349	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188127	1.00[ASN][1000 genomes]
rs280894	1.00[ASN][1000 genomes]
rs35453094	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427227	1.00[ASN][1000 genomes]
rs432933	1.00[ASN][1000 genomes]
rs56661363	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6681258	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689348	1.00[ASN][1000 genomes]
rs6695423	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71500673	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524020	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs795569	1.00[ASN][1000 genomes]
rs795571	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871743	chr1:75235082-75714554	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3368999	chr1:75524762-75933220	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75595200-75597400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
2	chr1:75595200-75597400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
3	chr1:75595400-75597400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
4	chr1:75595600-75597400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:75595600-75597800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
6	chr1:75595800-75597600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
7	chr1:75595800-75597600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr1:75595800-75598000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:75596000-75600600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
10	chr1:75596200-75597400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:75596200-75597400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:75596200-75598200	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:75596400-75600200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:75596800-75597400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:75596800-75597400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
16	chr1:75596800-75598000	Bivalent Enhancer	Fetal Brain Female	brain
17	chr1:75597000-75597800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
18	chr1:75597000-75597800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:75597000-75598000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
20	chr1:75597000-75598000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
21	chr1:75597200-75597400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
22	chr1:75597200-75597400	Bivalent Enhancer	Esophagus	oesophagus
23	chr1:75597200-75597400	Bivalent Enhancer	Right Ventricle	heart
24	chr1:75597200-75597600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:75597200-75597600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
26	chr1:75597200-75597800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell

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