Variant report

Variant	rs12030479
Chromosome Location	chr1:10920165-10920166
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10919663..10923359-chr1:10925488..10928766,3	MCF-7	breast:
2	chr1:10908264..10910893-chr1:10918893..10922550,4	K562	blood:
3	chr1:10918685..10920467-chr1:10928857..10931525,2	K562	blood:
4	chr1:10912236..10914687-chr1:10919102..10920834,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12023250	0.94[ASN][1000 genomes]
rs12028719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12033201	0.82[EUR][1000 genomes]
rs12048262	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142503	1.00[AMR][1000 genomes]
rs12724489	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12724989	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12731652	1.00[AMR][1000 genomes]
rs12740860	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34217099	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34542452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34896200	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35126763	1.00[AMR][1000 genomes]
rs35236487	0.83[EUR][1000 genomes]
rs35261279	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35414554	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35677622	1.00[AMR][1000 genomes]
rs35858703	1.00[AMR][1000 genomes]
rs36047809	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71509069	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529981	chr1:10697093-11353487	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	esv2757723	chr1:10742502-11055147	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2758921	chr1:10742502-11055147	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv871617	chr1:10858746-10935232	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv871155	chr1:10858746-10998509	Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv1825837	chr1:10887923-11093741	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv832425	chr1:10903845-11122975	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv545406	chr1:10915507-10935232	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	6 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	chr1:10914000-10920800	Weak transcription	Gastric	stomach
2	chr1:10917400-10921600	Weak transcription	Right Atrium	heart
3	chr1:10918600-10920400	Weak transcription	Right Ventricle	heart
4	chr1:10918600-10920600	Weak transcription	Fetal Heart	heart
5	chr1:10918600-10920600	Weak transcription	Left Ventricle	heart
6	chr1:10918600-10923000	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr1:10918600-10926600	Weak transcription	Esophagus	oesophagus
8	chr1:10918800-10920600	Weak transcription	Psoas Muscle	Psoas
9	chr1:10918800-10920800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:10919000-10920800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr1:10919600-10922200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:10919800-10920600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:10919800-10920600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr1:10919800-10920800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr1:10919800-10920800	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:10919800-10920800	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr1:10919800-10921000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:10919800-10921200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:10920000-10920200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr1:10920000-10920600	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr1:10920000-10926800	Bivalent Enhancer	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links