Variant report

Variant	rs653576
Chromosome Location	chr12:50452708-50452709
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr12:50449506-50452883	SK-N-SH	brain:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50450867..50453197-chr12:50472058..50474772,2	MCF-7	breast:
2	chr12:50450859..50453547-chr12:50463168..50465511,2	MCF-7	breast:
3	chr12:50450302..50454051-chr12:50467339..50469182,3	K562	blood:
4	chr12:50392906..50394750-chr12:50452166..50454470,2	MCF-7	breast:
5	chr12:50452237..50453974-chr12:50505551..50507211,2	K562	blood:
6	chr12:50451739..50453323-chr12:50478566..50480871,2	MCF-7	breast:
7	chr12:50452539..50455408-chr12:50466138..50467868,2	MCF-7	breast:
8	chr12:50452088..50458692-chr12:50460164..50465883,8	K562	blood:
9	chr12:50360045..50361666-chr12:50451717..50454140,2	MCF-7	breast:
10	chr12:50348029..50350628-chr12:50451106..50452724,2	MCF-7	breast:

No data

Variant related genes	Relation type
ASIC1	TF binding region
ENSG00000086159	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000161800	Chromatin interaction
ENSG00000272368	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000257378	Chromatin interaction

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

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

rs_ID	r²[population]
rs376184	0.85[ASN][1000 genomes]
rs386469	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs393848	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs404751	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs439171	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs450423	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs484951	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs590460	0.90[ASN][1000 genomes]
rs613066	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs627869	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs627887	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs706789	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs706794	0.85[ASN][1000 genomes]
rs835591	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs835593	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs835594	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836184	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs836185	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs836186	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs844359	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs860699	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised 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	28 gene(s)	inside rSNPs	diseases
6	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription 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	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50451000-50452800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr12:50451200-50452800	Active TSS	Stomach Smooth Muscle	stomach
3	chr12:50451400-50454400	Enhancers	Fetal Brain Male	brain
4	chr12:50451400-50459800	Weak transcription	Fetal Heart	heart
5	chr12:50451400-50464000	Weak transcription	Fetal Lung	lung
6	chr12:50451800-50453600	Weak transcription	HSMMtube	muscle
7	chr12:50451800-50454200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:50451800-50454200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:50451800-50464200	Weak transcription	Gastric	stomach
10	chr12:50452000-50452800	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr12:50452000-50452800	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr12:50452000-50452800	Flanking Active TSS	Fetal Brain Female	brain
13	chr12:50452000-50452800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
14	chr12:50452000-50453000	Flanking Active TSS	Brain Germinal Matrix	brain
15	chr12:50452000-50453000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
16	chr12:50452000-50454600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr12:50452000-50455000	Weak transcription	Right Atrium	heart
18	chr12:50452000-50456200	Weak transcription	HMEC	breast
19	chr12:50452000-50464200	Weak transcription	A549	lung
20	chr12:50452200-50453400	Weak transcription	NH-A	brain
21	chr12:50452200-50453600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:50452200-50453800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr12:50452200-50454600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr12:50452200-50454600	Weak transcription	Adipose Nuclei	Adipose
25	chr12:50452200-50456400	Weak transcription	HSMM	muscle
26	chr12:50452200-50464000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:50452400-50452800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:50452400-50452800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:50452400-50452800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr12:50452400-50452800	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr12:50452400-50452800	Enhancers	Brain Substantia Nigra	brain
32	chr12:50452400-50452800	Bivalent Enhancer	Fetal Thymus	thymus
33	chr12:50452400-50453000	Weak transcription	Fetal Intestine Small	intestine
34	chr12:50452400-50453400	Enhancers	Brain Hippocampus Middle	brain
35	chr12:50452400-50453800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:50452400-50454000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:50452400-50454200	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr12:50452400-50454400	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr12:50452400-50455200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr12:50452400-50460200	Weak transcription	Hela-S3	cervix
41	chr12:50452600-50452800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:50452600-50452800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:50452600-50452800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:50452600-50452800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:50452600-50452800	Enhancers	Brain Cingulate Gyrus	brain
46	chr12:50452600-50452800	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:50452600-50453000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:50452600-50453200	Enhancers	Primary T cells from cord blood	blood
49	chr12:50452600-50453400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:50452600-50453800	Enhancers	Brain Angular Gyrus	brain

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