Variant report

Variant	rs3931457
Chromosome Location	chr1:46842583-46842584
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46840775..46843213-chr1:46874405..46877016,2	K562	blood:
2	chr1:46840664..46843156-chr1:46846498..46848790,3	K562	blood:
3	chr1:46840664..46844647-chr1:46845051..46848530,4	K562	blood:
4	chr1:46780681..46783064-chr1:46842427..46844365,2	K562	blood:

Variant related genes	Relation type
ENSG00000117480	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11211267	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11802856	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11804220	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11804982	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12086460	1.00[EUR][1000 genomes]
rs12096333	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35563048	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57638901	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6678791	0.97[AFR][1000 genomes]
rs6688130	0.83[AMR][1000 genomes]
rs6703596	0.90[AFR][1000 genomes];1.00[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	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers 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	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS 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	72 gene(s)	inside rSNPs	diseases
3	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
4	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv546162	chr1:46807597-46870761	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46807600-46844600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:46809200-46848600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:46828200-46845400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:46828600-46843800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:46829200-46846400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:46829200-46847200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:46829200-46847600	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:46829200-46848000	Weak transcription	Ovary	ovary
9	chr1:46829400-46859400	Weak transcription	Brain Substantia Nigra	brain
10	chr1:46830600-46848800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:46833400-46845600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:46834600-46847800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:46834600-46859600	Weak transcription	Psoas Muscle	Psoas
14	chr1:46834800-46842600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:46834800-46844400	Weak transcription	Lung	lung
16	chr1:46834800-46844800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:46834800-46846200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:46834800-46846800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:46834800-46847600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:46834800-46848600	Weak transcription	Fetal Stomach	stomach
21	chr1:46834800-46853800	Weak transcription	Brain Anterior Caudate	brain
22	chr1:46835000-46847600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:46835400-46845800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:46836000-46847200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:46836200-46845600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:46836200-46845600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:46836200-46845800	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:46836200-46859400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:46836600-46843200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:46836600-46848800	Weak transcription	Primary T cells from cord blood	blood
31	chr1:46836800-46848800	Weak transcription	Adipose Nuclei	Adipose
32	chr1:46839400-46847600	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:46839400-46848400	Weak transcription	Placenta	Placenta
34	chr1:46839400-46848800	Weak transcription	Fetal Intestine Small	intestine
35	chr1:46839400-46858600	Weak transcription	Right Atrium	heart
36	chr1:46839600-46848600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr1:46841400-46843200	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links