Variant report

Variant	rs12042481
Chromosome Location	chr1:45964766-45964767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45964582-45967225	HepG2	liver:	n/a	n/a
2	STAT1	chr1:45964706-45964768	GM12878	blood:	n/a	n/a
3	SREBP1	chr1:45964570-45967128	GM12878	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45804114..45807301-chr1:45961577..45967419,8	K562	blood:
2	chr1:45185969..45188598-chr1:45964540..45967567,4	K562	blood:
3	chr1:45283510..45287262-chr1:45964108..45968951,6	K562	blood:
4	chr1:45806085..45807923-chr1:45963911..45966246,2	MCF-7	breast:
5	chr1:45768003..45772070-chr1:45964648..45967315,5	K562	blood:
6	chr1:45963397..45969763-chr1:46047572..46053150,23	K562	blood:
7	chr1:45963437..45971807-chr1:46047572..46053150,22	K562	blood:
8	chr1:45265558..45267516-chr1:45964222..45967034,2	K562	blood:
9	chr1:45954905..45960579-chr1:45960652..45966878,10	K562	blood:
10	chr1:45964150..45967582-chr1:46014583..46018871,5	K562	blood:
11	chr1:45272934..45277358-chr1:45964626..45967668,4	K562	blood:
12	chr1:45284392..45287262-chr1:45964108..45967526,3	K562	blood:

No data

Variant related genes	Relation type
CCDC163P	TF binding region
MMACHC	TF binding region
ENSG00000132781	Chromatin interaction
ENSG00000070759	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000188396	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1006215	1.00[JPT][hapmap]
rs1044717	0.88[ASN][1000 genomes]
rs10493120	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs1053941	1.00[ASW][hapmap]
rs1088099	1.00[ASN][1000 genomes]
rs11211110	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs11211115	1.00[JPT][hapmap]
rs11211132	0.91[CHD][hapmap]
rs11211133	0.88[ASN][1000 genomes]
rs11579176	1.00[ASW][hapmap]
rs12021717	0.88[ASN][1000 genomes]
rs12047498	1.00[ASN][1000 genomes]
rs12145526	0.85[ASN][1000 genomes]
rs12729974	0.86[ASN][1000 genomes]
rs1337902	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs1494813	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs1691217	1.00[JPT][hapmap]
rs1771549	1.00[JPT][hapmap]
rs2065708	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs2356559	0.90[CHD][hapmap]
rs2991966	0.88[ASN][1000 genomes]
rs3219487	1.00[MEX][hapmap]
rs3748643	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3748644	1.00[JPT][hapmap]
rs4660306	0.91[CHD][hapmap]
rs4660860	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs4660862	0.85[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs4660864	0.85[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs56261438	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6429567	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs6662572	1.00[ASW][hapmap]
rs6667191	0.88[ASN][1000 genomes]
rs6688516	0.88[ASN][1000 genomes]
rs7516006	0.88[ASN][1000 genomes]
rs7539253	0.85[ASN][1000 genomes]
rs7543076	1.00[ASN][1000 genomes]
rs7546268	1.00[ASN][1000 genomes]
rs7553374	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs781057	1.00[JPT][hapmap]
rs781062	1.00[JPT][hapmap]
rs781066	0.94[ASN][1000 genomes]
rs937290	0.85[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs945179	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[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	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs12042481	CCDC163P	cis	lung	GTEx
rs12042481	CCDC163P	cis	Muscle Skeletal	GTEx
rs12042481	CCDC163P	cis	Whole Blood	GTEx
rs12042481	CCDC163P	cis	Artery Aorta	GTEx
rs12042481	CCDC163P	cis	Esophagus Mucosa	GTEx
rs12042481	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs12042481	NSUN4	cis	lymphoblastoid	seeQTL
rs12042481	CCDC163P	cis	Thyroid	GTEx
rs12042481	CCDC163P	cis	Esophagus Muscularis	GTEx
rs12042481	CCDC163P	cis	Artery Tibial	GTEx
rs12042481	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs12042481	TESK2	cis	lymphoblastoid	seeQTL
rs12042481	CCDC163P	cis	Heart Left Ventricle	GTEx
rs12042481	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs12042481	CCDC163P	cis	Nerve Tibial	GTEx
rs12042481	CCDC163P	cis	Stomach	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45956800-45964800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:45956800-45964800	Weak transcription	Spleen	Spleen
3	chr1:45956800-45965000	Weak transcription	Gastric	stomach
4	chr1:45956800-45974000	Weak transcription	Small Intestine	intestine
5	chr1:45957000-45964800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:45957400-45965200	Weak transcription	HSMM	muscle
7	chr1:45957600-45964800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:45957600-45964800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:45957600-45964800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:45957600-45965000	Weak transcription	Psoas Muscle	Psoas
11	chr1:45957800-45964800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:45957800-45964800	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:45957800-45965000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:45957800-45965000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:45958000-45964800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:45958000-45964800	Weak transcription	Adipose Nuclei	Adipose
17	chr1:45958800-45964800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr1:45958800-45964800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:45961000-45964800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:45961200-45964800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:45962400-45964800	Weak transcription	Primary T cells from cord blood	blood
22	chr1:45962400-45964800	Weak transcription	Esophagus	oesophagus
23	chr1:45962400-45965000	Weak transcription	Right Atrium	heart
24	chr1:45962600-45964800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:45962600-45964800	Weak transcription	Lung	lung
26	chr1:45962600-45965000	Weak transcription	Left Ventricle	heart
27	chr1:45963000-45964800	Weak transcription	Placenta	Placenta
28	chr1:45963200-45965200	Weak transcription	Aorta	Aorta
29	chr1:45964000-45964800	Enhancers	Brain Hippocampus Middle	brain
30	chr1:45964000-45964800	Enhancers	Brain Substantia Nigra	brain
31	chr1:45964000-45964800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr1:45964000-45965000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:45964000-45965000	Enhancers	Liver	Liver
34	chr1:45964000-45965000	Enhancers	Brain Cingulate Gyrus	brain
35	chr1:45964000-45965000	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr1:45964000-45965000	Flanking Active TSS	HepG2	liver
37	chr1:45964200-45964800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:45964200-45964800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:45964200-45964800	Enhancers	K562	blood
40	chr1:45964200-45965000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:45964200-45965000	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr1:45964200-45965000	Enhancers	Primary T cells fromperipheralblood	blood
43	chr1:45964200-45965000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:45964200-45965000	Enhancers	Fetal Stomach	stomach
45	chr1:45964200-45965200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:45964400-45964800	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr1:45964400-45964800	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr1:45964400-45964800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:45964400-45964800	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr1:45964400-45964800	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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