Variant report

Variant	rs59834392
Chromosome Location	chr1:45093761-45093762
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45089432..45094163-chr1:45095736..45099125,6	MCF-7	breast:
2	chr1:45086647..45106769-chr1:45179099..45192041,56	K562	blood:

Variant related genes	Relation type
ENSG00000198520	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000187147	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11582970	0.85[ASN][1000 genomes]
rs12036630	0.90[EUR][1000 genomes]
rs12728857	0.85[ASN][1000 genomes]
rs1321703	0.90[EUR][1000 genomes]
rs16832186	0.90[EUR][1000 genomes]
rs16832188	0.90[EUR][1000 genomes]
rs2355365	0.85[ASN][1000 genomes]
rs3738733	1.00[EUR][1000 genomes]
rs3754421	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768438	1.00[EUR][1000 genomes]
rs3768441	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850854	0.90[EUR][1000 genomes]
rs3889695	0.90[EUR][1000 genomes]
rs41524944	0.90[EUR][1000 genomes]
rs4660286	0.90[EUR][1000 genomes]
rs4660814	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660819	0.90[EUR][1000 genomes]
rs56756630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57618636	0.97[AFR][1000 genomes]
rs66509359	0.90[EUR][1000 genomes]
rs72671943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72671944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72671945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72671948	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72671949	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72671950	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72671954	0.85[ASN][1000 genomes]
rs72671962	0.90[EUR][1000 genomes]
rs72671966	0.90[EUR][1000 genomes]
rs72671967	0.90[EUR][1000 genomes]
rs72671971	0.90[EUR][1000 genomes]
rs72671974	0.90[EUR][1000 genomes]
rs72671982	0.90[EUR][1000 genomes]
rs72671984	0.90[EUR][1000 genomes]
rs72671988	0.90[EUR][1000 genomes]
rs7532001	0.90[EUR][1000 genomes]
rs7539607	0.90[EUR][1000 genomes]
rs995089	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv461395	chr1:44898998-45119965	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
5	nsv546144	chr1:44898998-45119965	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer 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	27 gene(s)	inside rSNPs	diseases
6	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
7	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45074800-45096800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:45079600-45096800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:45083000-45097000	Weak transcription	Spleen	Spleen
4	chr1:45083400-45097200	Weak transcription	Gastric	stomach
5	chr1:45083600-45097000	Weak transcription	Right Atrium	heart
6	chr1:45083800-45096600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:45083800-45096600	Weak transcription	Fetal Heart	heart
8	chr1:45084200-45097000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:45084800-45096800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:45085600-45097000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:45085600-45097000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:45085800-45096600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:45085800-45096800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:45087200-45096800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:45087600-45093800	Weak transcription	Brain Substantia Nigra	brain
16	chr1:45087600-45094400	Weak transcription	NH-A	brain
17	chr1:45087600-45096600	Weak transcription	Brain Angular Gyrus	brain
18	chr1:45087800-45096400	Weak transcription	Brain Anterior Caudate	brain
19	chr1:45087800-45096800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:45088400-45094000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:45088400-45094600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:45088600-45094000	Weak transcription	Osteobl	bone
23	chr1:45089000-45093800	Weak transcription	NHDF-Ad	bronchial
24	chr1:45089800-45097000	Weak transcription	Psoas Muscle	Psoas
25	chr1:45090800-45096800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:45091000-45096600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:45091200-45094200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:45091400-45097000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:45091400-45097000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr1:45091600-45096600	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:45091800-45096200	Strong transcription	Brain Hippocampus Middle	brain
32	chr1:45091800-45096400	Strong transcription	Brain Cingulate Gyrus	brain
33	chr1:45091800-45097000	Weak transcription	Fetal Brain Female	brain
34	chr1:45092000-45096800	Weak transcription	Fetal Brain Male	brain
35	chr1:45092000-45097000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:45092200-45094800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:45093200-45097000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:45093400-45094600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:45093600-45096600	Enhancers	K562	blood
40	chr1:45093600-45097200	Enhancers	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links