Variant report

Variant	rs2429168
Chromosome Location	chr12:2028482-2028483
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:2028475-2028525	AG10803	skin:	n/a
2	chr12:2028475-2028525	BE2_C	brain:	n/a
3	chr12:2028475-2028525	GM12891	blood:	n/a
4	chr12:2028475-2028525	HEK293	kidney:	embryo
5	chr12:2028475-2028525	HCPEpiC	choroid plexus:	n/a
6	chr12:2028475-2028525	HUVEC	blood vessel:	n/a
7	chr12:2028475-2028525	U87	brain:	n/a
8	chr12:2028475-2028525	PFSK-1	brain:	n/a
9	chr12:2028475-2028525	HRCEpiC	kidney:	n/a
10	chr12:2028475-2028525	HNPCEpiC	eye:	n/a
11	chr12:2028475-2028525	SK-N-SH_RA	brain:	n/a
12	chr12:2028475-2028525	GM19239	blood:	n/a
13	chr12:2028475-2028525	HepG2	liver:	n/a
14	chr12:2028475-2028525	NHDF-neo	bronchial:	n/a
15	chr12:2028475-2028525	HCM	heart:	n/a
16	chr12:2028475-2028525	HIPEpiC	eye:	n/a
17	chr12:2028475-2028525	Caco-2	colon:	n/a
18	chr12:2028475-2028525	HEEpiC	esophagus:	n/a
19	chr12:2028475-2028525	BJ	skin:	n/a
20	chr12:2028475-2028525	IMR90	lung:	fetal
21	chr12:2028475-2028525	ProgFib	skin:	n/a
22	chr12:2028475-2028525	Hepatocyte	liver:	n/a
23	chr12:2028475-2028525	PANC-1	pancreas:	n/a
24	chr12:2028475-2028525	NB4	blood:	n/a
25	chr12:2028475-2028525	MCF-7	breast:	n/a
26	chr12:2028475-2028525	PrEC	prostate:	n/a
27	chr12:2028475-2028525	GM12878	blood:	n/a
28	chr12:2028475-2028525	MCF10A-Er-Src	breast:	n/a
29	chr12:2028475-2028525	HAEpiC	amniotic membrane:	n/a
30	chr12:2028475-2028525	ovcar-3	ovarian:	n/a
31	chr12:2028475-2028525	RPTEC	kidney:	n/a
32	chr12:2028475-2028525	HCT-116	colon:	n/a
33	chr12:2028475-2028525	NH-A	brain:	n/a
34	chr12:2028475-2028525	AG09309	skin:	n/a
35	chr12:2028475-2028525	HL-60	blood:	n/a
36	chr12:2028475-2028525	ECC-1	luminal epithelium:	n/a
37	chr12:2028475-2028525	T-47D	breast:	n/a
38	chr12:2028475-2028525	Jurkat	blood:	n/a
39	chr12:2028475-2028525	SK-N-MC	brain:	n/a
40	chr12:2028475-2028525	AG04449	skin:	fetal
41	chr12:2028475-2028525	HMEC	breast:	n/a
42	chr12:2028475-2028525	SAEC	small airway:	n/a
43	chr12:2028475-2028525	AG04450	lung:	fetal
44	chr12:2028475-2028525	CMK	blood:	n/a
45	chr12:2028475-2028525	HRE	kidney:	n/a
46	chr12:2028475-2028525	AoSMC	blood vessel:	n/a
47	chr12:2028475-2028525	H1-hESC	embryonic stem cell:	embryo
48	chr12:2028475-2028525	LNCaP	prostate:	n/a
49	chr12:2028475-2028525	SK-N-SH	brain:	n/a
50	chr12:2028475-2028525	AG09319	gingival:	n/a

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

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

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

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

No data

Variant related genes	Relation type
CACNA2D4	CpG island
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]
rs2429169	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2429184	1.00[ASN][1000 genomes]
rs2470409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];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:42 , 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	chr12:2026000-2028800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:2026400-2028600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:2026400-2028800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:2026600-2028600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr12:2026600-2028600	Flanking Active TSS	Primary B cells from peripheral blood	blood
8	chr12:2026600-2030200	Weak transcription	Pancreas	Pancrea
9	chr12:2026600-2031600	Weak transcription	Gastric	stomach
10	chr12:2026800-2028800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr12:2026800-2033600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:2027000-2028600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:2027000-2028600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr12:2027000-2028600	Active TSS	Duodenum Mucosa	Duodenum
15	chr12:2027200-2033800	Weak transcription	Colon Smooth Muscle	Colon
16	chr12:2027400-2028800	Enhancers	K562	blood
17	chr12:2027600-2028600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr12:2027600-2028600	Enhancers	Fetal Stomach	stomach
19	chr12:2027600-2029000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr12:2027600-2033600	Weak transcription	Left Ventricle	heart
21	chr12:2027600-2033600	Weak transcription	Right Ventricle	heart
22	chr12:2027600-2041800	Weak transcription	Fetal Brain Female	brain
23	chr12:2027800-2028600	Enhancers	Placenta	Placenta
24	chr12:2027800-2028800	Enhancers	Fetal Muscle Trunk	muscle
25	chr12:2027800-2028800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr12:2027800-2029000	Enhancers	Primary hematopoietic stem cells	blood
27	chr12:2027800-2029000	Enhancers	Fetal Muscle Leg	muscle
28	chr12:2027800-2029200	Enhancers	Fetal Thymus	thymus
29	chr12:2027800-2029200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr12:2027800-2033800	Weak transcription	Spleen	Spleen
31	chr12:2028000-2028800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:2028000-2028800	Enhancers	Thymus	Thymus
33	chr12:2028000-2029200	Enhancers	Primary B cells from cord blood	blood
34	chr12:2028000-2030400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr12:2028200-2028800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:2028200-2028800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:2028200-2030000	Weak transcription	Adipose Nuclei	Adipose
38	chr12:2028200-2030200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr12:2028200-2030200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:2028400-2031400	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr12:2028400-2033600	Weak transcription	Brain Anterior Caudate	brain
42	chr12:2028400-2033600	Weak transcription	Psoas Muscle	Psoas

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