Variant report

Variant	rs2470409
Chromosome Location	chr12:2028322-2028323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:2026369-2028390	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:2023041..2025540-chr12:2026529..2030092,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CACNA1C-1	chr12:2027014-2029505	NONHSAT025434

Variant related genes	Relation type
CACNA2D4	TF binding region
ENSG00000151062	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10735005	1.00[ASN][1000 genomes]
rs11062010	1.00[ASN][1000 genomes]
rs1558141	1.00[ASN][1000 genomes]
rs1558142	1.00[ASN][1000 genomes]
rs1990232	1.00[ASN][1000 genomes]
rs2008352	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013064	1.00[ASN][1000 genomes]
rs2429158	1.00[ASN][1000 genomes]
rs2429159	1.00[ASN][1000 genomes]
rs2429163	1.00[ASN][1000 genomes]
rs2429164	1.00[ASN][1000 genomes]
rs2429167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429169	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2429184	1.00[ASN][1000 genomes]
rs2470415	0.85[EUR][1000 genomes]
rs2470438	1.00[ASN][1000 genomes]
rs2906892	1.00[ASN][1000 genomes]
rs720456	1.00[ASN][1000 genomes]
rs758157	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758158	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181666	1.00[ASN][1000 genomes]
rs8181681	1.00[ASN][1000 genomes]
rs8181786	1.00[ASN][1000 genomes]
rs886939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886941	1.00[AFR][1000 genomes];1.00[AMR][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	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv898598	chr12:1939252-2215448	Strong transcription Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1046388	chr12:1964846-2034887	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1043329	chr12:1986238-2034887	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv557000	chr12:2008548-2045640	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv898600	chr12:2020045-2056363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2022600-2028800	Enhancers	Fetal Heart	heart
2	chr12:2024000-2029000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:2025600-2028400	Enhancers	Right Atrium	heart
4	chr12:2026000-2028800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:2026400-2028400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr12:2026400-2028600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:2026400-2028800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:2026600-2028400	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr12:2026600-2028600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr12:2026600-2028600	Flanking Active TSS	Primary B cells from peripheral blood	blood
11	chr12:2026600-2030200	Weak transcription	Pancreas	Pancrea
12	chr12:2026600-2031600	Weak transcription	Gastric	stomach
13	chr12:2026800-2028800	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr12:2026800-2033600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:2027000-2028600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:2027000-2028600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr12:2027000-2028600	Active TSS	Duodenum Mucosa	Duodenum
18	chr12:2027200-2033800	Weak transcription	Colon Smooth Muscle	Colon
19	chr12:2027400-2028400	Enhancers	Psoas Muscle	Psoas
20	chr12:2027400-2028800	Enhancers	K562	blood
21	chr12:2027600-2028600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr12:2027600-2028600	Enhancers	Fetal Stomach	stomach
23	chr12:2027600-2029000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr12:2027600-2033600	Weak transcription	Left Ventricle	heart
25	chr12:2027600-2033600	Weak transcription	Right Ventricle	heart
26	chr12:2027600-2041800	Weak transcription	Fetal Brain Female	brain
27	chr12:2027800-2028400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
28	chr12:2027800-2028600	Enhancers	Placenta	Placenta
29	chr12:2027800-2028800	Enhancers	Fetal Muscle Trunk	muscle
30	chr12:2027800-2028800	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr12:2027800-2029000	Enhancers	Primary hematopoietic stem cells	blood
32	chr12:2027800-2029000	Enhancers	Fetal Muscle Leg	muscle
33	chr12:2027800-2029200	Enhancers	Fetal Thymus	thymus
34	chr12:2027800-2029200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr12:2027800-2033800	Weak transcription	Spleen	Spleen
36	chr12:2028000-2028400	Enhancers	Brain Anterior Caudate	brain
37	chr12:2028000-2028800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr12:2028000-2028800	Enhancers	Thymus	Thymus
39	chr12:2028000-2029200	Enhancers	Primary B cells from cord blood	blood
40	chr12:2028000-2030400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr12:2028200-2028800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:2028200-2028800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:2028200-2030000	Weak transcription	Adipose Nuclei	Adipose
44	chr12:2028200-2030200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr12:2028200-2030200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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