Variant report

Variant	rs12129193
Chromosome Location	chr1:75597485-75597486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

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	SUZ12	chr1:75595125-75598694	H1-hESC	embryonic stem cell:	n/a	n/a
3	SUZ12	chr1:75594519-75601637	NT2-D1	testis:	n/a	n/a
4	POLR2A	chr1:75596570-75599860	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr1:75596503-75602546	H1-neurons	neurons:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:75597485-75597535	HepG2	liver:	n/a
2	chr1:75597485-75597535	HPAEpiC	pulmonary alveolar:	n/a
3	chr1:75597485-75597535	SKMC	muscle:	n/a
4	chr1:75597485-75597535	HCM	heart:	n/a
5	chr1:75597485-75597535	Hela-S3	cervix:	n/a
6	chr1:75597485-75597535	NT2-D1	testis:	n/a
7	chr1:75597485-75597535	HCF	heart:	n/a
8	chr1:75597485-75597535	A549	lung:	n/a
9	chr1:75597485-75597535	HCPEpiC	choroid plexus:	n/a
10	chr1:75597485-75597535	SK-N-MC	brain:	n/a
11	chr1:75597485-75597535	HRPEpiC	eye:	n/a
12	chr1:75597485-75597535	MCF10A-Er-Src	breast:	n/a
13	chr1:75597485-75597535	PANC-1	pancreas:	n/a
14	chr1:75597485-75597535	GM12892	blood:	n/a
15	chr1:75597485-75597535	H1-hESC	embryonic stem cell:	embryo
16	chr1:75597485-75597535	ovcar-3	ovarian:	n/a
17	chr1:75597485-75597535	Jurkat	blood:	n/a
18	chr1:75597485-75597535	NB4	blood:	n/a
19	chr1:75597485-75597535	K562	blood:	n/a
20	chr1:75597485-75597535	GM06990	blood:	n/a
21	chr1:75597485-75597535	PFSK-1	brain:	n/a
22	chr1:75597485-75597535	HRE	kidney:	n/a
23	chr1:75597485-75597535	HRCEpiC	kidney:	n/a
24	chr1:75597485-75597535	NH-A	brain:	n/a
25	chr1:75597485-75597535	Caco-2	colon:	n/a
26	chr1:75597485-75597535	GM19239	blood:	n/a
27	chr1:75597485-75597535	AG10803	skin:	n/a
28	chr1:75597485-75597535	NHDF-neo	bronchial:	n/a
29	chr1:75597485-75597535	SK-N-SH	brain:	n/a
30	chr1:75597485-75597535	HCT-116	colon:	n/a
31	chr1:75597485-75597535	HAEpiC	amniotic membrane:	n/a
32	chr1:75597485-75597535	AG09319	gingival:	n/a
33	chr1:75597485-75597535	HMEC	breast:	n/a
34	chr1:75597485-75597535	GM12878	blood:	n/a
35	chr1:75597485-75597535	CMK	blood:	n/a
36	chr1:75597485-75597535	RPTEC	kidney:	n/a
37	chr1:75597485-75597535	HNPCEpiC	eye:	n/a
38	chr1:75597485-75597535	ECC-1	luminal epithelium:	n/a
39	chr1:75597485-75597535	HUVEC	blood vessel:	n/a
40	chr1:75597485-75597535	IMR90	lung:	fetal
41	chr1:75597485-75597535	AG04449	skin:	fetal
42	chr1:75597485-75597535	SAEC	small airway:	n/a
43	chr1:75597485-75597535	AoSMC	blood vessel:	n/a
44	chr1:75597485-75597535	NHBE	bronchial:	n/a
45	chr1:75597485-75597535	HL-60	blood:	n/a
46	chr1:75597485-75597535	MCF-7	breast:	n/a
47	chr1:75597485-75597535	HEK293	kidney:	embryo
48	chr1:75597485-75597535	BE2_C	brain:	n/a
49	chr1:75597485-75597535	AG04450	lung:	fetal
50	chr1:75597485-75597535	Hepatocyte	liver:	n/a

No data

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

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

No data

Variant related genes	Relation type
LHX8	TF binding region
LHX8	CpG island

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

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

rs_ID	r²[population]
rs12129029	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129158	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133614	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138223	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142460	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12723906	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726443	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12729173	1.00[ASN][1000 genomes]
rs12732329	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12741928	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12751207	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526502	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526510	1.00[ASN][1000 genomes]
rs1526511	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1852348	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1852349	0.98[AMR][1000 genomes];0.96[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];0.98[AMR][1000 genomes];0.98[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];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6681258	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689348	1.00[ASN][1000 genomes]
rs6695423	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71500673	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524020	0.95[AMR][1000 genomes];0.96[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:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75595600-75597800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
2	chr1:75595800-75597600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
3	chr1:75595800-75597600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr1:75595800-75598000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:75596000-75600600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
6	chr1:75596200-75598200	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:75596400-75600200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:75596800-75598000	Bivalent Enhancer	Fetal Brain Female	brain
9	chr1:75597000-75597800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
10	chr1:75597000-75597800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:75597000-75598000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
12	chr1:75597000-75598000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
13	chr1:75597200-75597600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:75597200-75597600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
15	chr1:75597200-75597800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
16	chr1:75597400-75597600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
17	chr1:75597400-75597600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
18	chr1:75597400-75597600	Bivalent Enhancer	Brain Hippocampus Middle	brain
19	chr1:75597400-75598000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:75597400-75598200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:75597400-75599400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell

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