Variant report

Variant	rs4435493
Chromosome Location	chr2:55449318-55449319
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	CEBPB	chr2:55449272-55449493	A549	lung:	n/a	n/a
2	CEBPB	chr2:55449286-55449495	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55449257..55451239-chr2:55511673..55514610,2	MCF-7	breast:
2	chr2:55447982..55449746-chr2:55449877..55451589,2	MCF-7	breast:
3	chr2:55446836..55449379-chr2:55449395..55451739,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227799	TF binding region
ENSG00000162994	Chromatin interaction
ENSG00000206964	Chromatin interaction
ENSG00000227799	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10200120	0.82[ASN][1000 genomes]
rs1056445	0.91[CHB][hapmap];0.87[CHD][hapmap]
rs11357	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs11692206	0.89[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs12052613	0.81[ASN][1000 genomes]
rs12615414	0.81[AFR][1000 genomes]
rs12988617	0.91[ASN][1000 genomes]
rs17046778	0.83[AMR][1000 genomes]
rs17852670	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2576711	0.86[CHB][hapmap]
rs2576712	0.81[ASN][1000 genomes]
rs2589080	0.82[ASN][1000 genomes]
rs2589092	0.95[CHB][hapmap]
rs2589094	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs2589096	0.86[CHB][hapmap]
rs2864819	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2864826	0.80[ASN][1000 genomes]
rs2917779	0.85[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs2920967	0.80[ASN][1000 genomes]
rs34348115	0.83[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs34511570	0.93[ASN][1000 genomes]
rs56039135	0.94[ASN][1000 genomes]
rs6545480	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6706815	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737227	0.91[CHB][hapmap]
rs6755515	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71414550	0.86[AFR][1000 genomes]
rs72799507	0.81[ASN][1000 genomes]
rs7349405	0.86[CHD][hapmap]
rs7590143	0.84[CHD][hapmap]
rs934709	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs4435493	C2orf63	cis	multi-tissue	Pritchard
rs4435493	CLHC1	cis	Adipose Subcutaneous	GTEx
rs4435493	C2orf63	cis	lymphoblastoid	seeQTL
rs4435493	CLHC1	cis	Stomach	GTEx
rs4435493	SPTBN1	cis	multi-tissue	Pritchard
rs4435493	CLHC1	cis	Muscle Skeletal	GTEx
rs4435493	CLHC1	cis	Artery Aorta	GTEx
rs4435493	CLHC1	cis	Esophagus Muscularis	GTEx
rs4435493	C2orf63	cis	Lymphoblastoid	GTEx
rs4435493	C2orf63	cis	Liver	GTEx
rs4435493	CLHC1	cis	Whole Blood	GTEx
rs4435493	CLHC1	cis	Nerve Tibial	GTEx
rs4435493	AC012358.7	cis	Adipose Subcutaneous	GTEx
rs4435493	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs4435493	CLHC1	cis	lung	GTEx
rs4435493	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs4435493	CLHC1	cis	Skin Sun Exposed Lower leg	GTEx
rs4435493	CLHC1	cis	Thyroid	GTEx
rs4435493	FLJ31438	cis	multi-tissue	Pritchard
rs4435493	CLHC1	cis	Artery Tibial	GTEx
rs4435493	CLHC1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55397200-55450000	Weak transcription	NH-A	brain
2	chr2:55402800-55450000	Weak transcription	NHDF-Ad	bronchial
3	chr2:55415400-55450000	Weak transcription	GM12878-XiMat	blood
4	chr2:55416800-55450000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:55417400-55450200	Weak transcription	Placenta	Placenta
6	chr2:55417800-55450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:55424200-55450000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:55424600-55449800	Weak transcription	Thymus	Thymus
9	chr2:55424600-55450000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:55424600-55450200	Weak transcription	Brain Germinal Matrix	brain
11	chr2:55424600-55451200	Weak transcription	HepG2	liver
12	chr2:55424800-55450200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:55425600-55449800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:55427400-55450200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:55427400-55450200	Weak transcription	Aorta	Aorta
16	chr2:55427400-55450600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:55427400-55450600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:55429200-55449800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:55430000-55450400	Weak transcription	Left Ventricle	heart
20	chr2:55432000-55449800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:55432000-55451200	Weak transcription	Dnd41	blood
22	chr2:55432200-55450000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:55432800-55450000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:55432800-55450000	Weak transcription	Fetal Stomach	stomach
25	chr2:55433000-55449800	Weak transcription	Pancreas	Pancrea
26	chr2:55433000-55450200	Weak transcription	Ovary	ovary
27	chr2:55433400-55450000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:55441200-55450000	Weak transcription	K562	blood
29	chr2:55441400-55450000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:55444400-55450400	Weak transcription	Gastric	stomach
31	chr2:55444600-55449800	Weak transcription	Fetal Intestine Small	intestine
32	chr2:55446000-55450000	Weak transcription	HUVEC	blood vessel
33	chr2:55446800-55450200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:55447200-55450000	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr2:55447600-55450000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr2:55447800-55450400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:55448000-55449400	Strong transcription	HSMM	muscle
38	chr2:55448200-55449600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:55448400-55449400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr2:55448400-55449400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:55448400-55449800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr2:55448400-55450200	Weak transcription	Psoas Muscle	Psoas
43	chr2:55448600-55449400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:55448600-55449600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:55448600-55449800	Weak transcription	Primary T cells from cord blood	blood
46	chr2:55448600-55449800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:55448600-55450000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:55448800-55449400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:55448800-55449400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:55448800-55449400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links