Variant report

Variant	rs1258030
Chromosome Location	chr1:47009757-47009758
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:47008125..47011332-chr1:47013107..47016538,3	K562	blood:
2	chr1:46999948..47005205-chr1:47009363..47015200,7	K562	blood:
3	chr1:47009141..47012032-chr1:47183376..47185595,2	K562	blood:
4	chr1:47005992..47007886-chr1:47008521..47010850,2	MCF-7	breast:
5	chr1:47009625..47011332-chr1:47012980..47015452,2	K562	blood:
6	chr1:46992147..46995347-chr1:47008706..47012363,4	K562	blood:
7	chr1:46920354..46923380-chr1:47007793..47010498,3	K562	blood:
8	chr1:47008373..47012047-chr1:47032869..47035437,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000079277	Chromatin interaction
ENSG00000159658	Chromatin interaction
ENSG00000225667	Chromatin interaction
ENSG00000162456	Chromatin interaction
ENSG00000269956	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12142727	0.92[EUR][1000 genomes]
rs12145313	0.94[EUR][1000 genomes]
rs1258031	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1258032	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1258033	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1258034	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258035	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1258044	0.89[EUR][1000 genomes]
rs1923810	0.93[EUR][1000 genomes]
rs4660356	0.92[EUR][1000 genomes]
rs7523809	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv998422	chr1:46969626-47023671	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv534953	chr1:46969626-47023671	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1010578	chr1:46977818-47010579	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1009899	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	nsv534954	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv1008246	chr1:47007844-47069845	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46999600-47035000	Weak transcription	Right Atrium	heart
2	chr1:47007400-47009800	Bivalent Enhancer	Fetal Brain Male	brain
3	chr1:47008400-47009800	Weak transcription	Pancreas	Pancrea
4	chr1:47009000-47010200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr1:47009000-47010400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:47009200-47010000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:47009200-47010000	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr1:47009200-47010200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr1:47009200-47010200	Bivalent Enhancer	Fetal Stomach	stomach
10	chr1:47009200-47010200	Enhancers	K562	blood
11	chr1:47009200-47010400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr1:47009200-47010400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr1:47009400-47009800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:47009400-47009800	Active TSS	Brain Angular Gyrus	brain
15	chr1:47009400-47009800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
16	chr1:47009400-47009800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
17	chr1:47009400-47010000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
18	chr1:47009400-47010000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
19	chr1:47009400-47010000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:47009400-47010200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
21	chr1:47009400-47010200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
22	chr1:47009400-47010200	Bivalent/Poised TSS	Fetal Brain Female	brain
23	chr1:47009400-47010200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
24	chr1:47009400-47010400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr1:47009400-47010400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:47009400-47010600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
27	chr1:47009600-47009800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
28	chr1:47009600-47009800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
29	chr1:47009600-47009800	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
30	chr1:47009600-47009800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
31	chr1:47009600-47010000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:47009600-47010000	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:47009600-47010000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:47009600-47010000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
35	chr1:47009600-47010000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
36	chr1:47009600-47010000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:47009600-47010000	Flanking Active TSS	Right Ventricle	heart
38	chr1:47009600-47010200	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:47009600-47010200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
40	chr1:47009600-47010200	Bivalent Enhancer	Placenta	Placenta
41	chr1:47009600-47010200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
42	chr1:47009600-47010400	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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