Variant report

Variant	rs58545634
Chromosome Location	chr12:46783870-46783871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46661608..46665145-chr12:46782795..46784493,3	MCF-7	breast:
2	chr12:46782810..46784901-chr12:46849696..46851269,2	MCF-7	breast:
3	chr12:46782004..46784906-chr12:46849046..46851285,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARID2-12	chr12:46782639-46785909	NONHSAT027878

Variant related genes	Relation type
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11183453	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11833812	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11834593	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1948425	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2307059	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55795804	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57199226	0.85[EUR][1000 genomes]
rs57786829	0.81[EUR][1000 genomes]
rs59546893	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73282593	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7967840	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46778200-46784800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:46778400-46784200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:46778400-46786800	Enhancers	NHDF-Ad	bronchial
4	chr12:46778600-46784200	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr12:46778600-46785400	Enhancers	Adipose Nuclei	Adipose
6	chr12:46778600-46787000	Enhancers	Fetal Lung	lung
7	chr12:46778800-46784000	Enhancers	Duodenum Mucosa	Duodenum
8	chr12:46778800-46797200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:46779600-46786000	Weak transcription	Gastric	stomach
10	chr12:46779600-46786400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:46779600-46786400	Weak transcription	Right Ventricle	heart
12	chr12:46779600-46802800	Weak transcription	Pancreas	Pancrea
13	chr12:46780400-46784400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:46780600-46786800	Weak transcription	Brain Substantia Nigra	brain
15	chr12:46780600-46788600	Weak transcription	Fetal Brain Male	brain
16	chr12:46780800-46784000	Weak transcription	Stomach Mucosa	stomach
17	chr12:46780800-46785600	Enhancers	Liver	Liver
18	chr12:46781000-46784400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:46781000-46784600	Weak transcription	Fetal Intestine Large	intestine
20	chr12:46781000-46785600	Flanking Active TSS	GM12878-XiMat	blood
21	chr12:46781200-46785600	Enhancers	HUVEC	blood vessel
22	chr12:46781400-46786600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:46781400-46787000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr12:46781400-46787200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:46781600-46784000	Enhancers	A549	lung
26	chr12:46781600-46789200	Weak transcription	Fetal Stomach	stomach
27	chr12:46781600-46795400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:46781800-46784000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr12:46781800-46784800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:46781800-46784800	Weak transcription	Esophagus	oesophagus
31	chr12:46781800-46784800	Weak transcription	Lung	lung
32	chr12:46781800-46785000	Genic enhancers	HUES64 Cell Line	embryonic stem cell
33	chr12:46781800-46785200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
34	chr12:46781800-46785400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:46781800-46785600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:46781800-46786400	Weak transcription	Colonic Mucosa	Colon
37	chr12:46781800-46786400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr12:46781800-46786400	Weak transcription	Left Ventricle	heart
39	chr12:46781800-46786600	Enhancers	NHLF	lung
40	chr12:46781800-46795000	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:46782000-46784000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:46782000-46784000	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr12:46782000-46784200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr12:46782000-46784200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:46782000-46784600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr12:46782000-46784800	Weak transcription	Right Atrium	heart
47	chr12:46782000-46784800	Weak transcription	Spleen	Spleen
48	chr12:46782000-46785000	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr12:46782000-46785000	Enhancers	Primary B cells from peripheral blood	blood
50	chr12:46782000-46785000	Enhancers	Skeletal Muscle Male	skeletal muscle

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