Variant report

Variant	rs4531260
Chromosome Location	chr1:227545868-227545869
allele	C/T
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	chr1:227500332..227503244-chr1:227542452..227546426,3	K562	blood:
2	chr1:227544961..227546777-chr1:227556862..227559703,3	K562	blood:
3	chr1:227545277..227548710-chr1:227557152..227561579,4	K562	blood:
4	chr1:227544242..227546740-chr1:227566888..227569637,2	K562	blood:
5	chr1:227530329..227533212-chr1:227543637..227546131,2	K562	blood:
6	chr1:227542971..227547040-chr1:227548442..227550941,4	K562	blood:
7	chr1:227545250..227546932-chr1:227614922..227616911,2	K562	blood:
8	chr1:227502375..227508330-chr1:227544221..227551404,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10458380	0.83[ASN][1000 genomes]
rs10753434	0.88[ASN][1000 genomes]
rs10799412	0.88[ASN][1000 genomes]
rs10916123	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10916124	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10916127	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916128	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916129	0.92[ASN][1000 genomes]
rs12022275	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12023427	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12028523	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12047964	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12057466	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062358	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081061	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12085773	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16847682	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16847690	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28654860	0.89[ASN][1000 genomes]
rs4075196	0.99[ASN][1000 genomes]
rs4075861	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4233226	0.82[ASN][1000 genomes]
rs4653497	0.99[ASN][1000 genomes]
rs4653498	0.99[ASN][1000 genomes]
rs4653826	0.82[ASN][1000 genomes]
rs4653828	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653831	0.93[ASN][1000 genomes]
rs59718661	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61833060	0.99[ASN][1000 genomes]
rs6690898	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67343057	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72632826	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72759365	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7519870	0.97[ASN][1000 genomes]
rs7540726	0.80[ASN][1000 genomes]
rs7540833	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7541775	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7553358	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7555764	0.88[ASN][1000 genomes]
rs7556096	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227542600-227547400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:227544000-227546200	Enhancers	Fetal Intestine Large	intestine
3	chr1:227544200-227546000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:227544200-227546000	Enhancers	Fetal Intestine Small	intestine
5	chr1:227544200-227546000	Enhancers	Stomach Mucosa	stomach
6	chr1:227544200-227546000	Enhancers	NHLF	lung
7	chr1:227544200-227546200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:227544200-227546400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:227544200-227546600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:227544200-227547600	Enhancers	Lung	lung
11	chr1:227544400-227546000	Enhancers	Placenta Amnion	Placenta Amnion
12	chr1:227544400-227546600	Enhancers	Right Atrium	heart
13	chr1:227544600-227547000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:227545000-227547000	Enhancers	Psoas Muscle	Psoas
15	chr1:227545200-227546000	Enhancers	HMEC	breast
16	chr1:227545200-227546200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:227545400-227546200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:227545600-227546000	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr1:227545600-227546000	Enhancers	NHEK	skin
20	chr1:227545600-227547400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:227545800-227546000	Enhancers	Muscle Satellite Cultured Cells	--
22	chr1:227545800-227546000	Enhancers	A549	lung
23	chr1:227545800-227546000	Enhancers	HSMM	muscle
24	chr1:227545800-227546200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:227545800-227546600	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:227545800-227546600	Enhancers	Hela-S3	cervix
27	chr1:227545800-227546600	Enhancers	HUVEC	blood vessel
28	chr1:227545800-227546800	Weak transcription	Gastric	stomach
29	chr1:227545800-227547200	Enhancers	K562	blood
30	chr1:227545800-227547400	Weak transcription	Brain Substantia Nigra	brain
31	chr1:227545800-227547600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:227545800-227550000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:227545800-227552600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:227545800-227571200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links