Variant report

Variant	rs6656460
Chromosome Location	chr1:246903460-246903461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246898340..246900023-chr1:246902071..246904016,2	K562	blood:
2	chr1:246851356..246854003-chr1:246902517..246904591,2	K562	blood:

Variant related genes	Relation type
ENSG00000235021	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13274	1.00[AMR][1000 genomes]
rs28488566	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28628394	0.83[AMR][1000 genomes]
rs4509613	1.00[MEX][hapmap]
rs6697063	0.90[ASW][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7418413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7529097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9287208	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv870294	chr1:246877043-246927940	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6656460	SCCPDH	cis	multi-tissue	Pritchard
rs6656460	CGI-49	cis	multi-tissue	Pritchard
rs6656460	SCCPDH	cis	lymphoblastoid	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246903800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
3	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr1:246888800-246904000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:246888800-246904800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:246889000-246929000	Weak transcription	Stomach Mucosa	stomach
7	chr1:246889600-246907000	Strong transcription	Fetal Muscle Trunk	muscle
8	chr1:246890200-246905000	Strong transcription	Duodenum Mucosa	Duodenum
9	chr1:246890200-246906600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:246890200-246913200	Strong transcription	Fetal Muscle Leg	muscle
11	chr1:246890400-246907400	Strong transcription	Stomach Smooth Muscle	stomach
12	chr1:246890400-246909000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:246890600-246905000	Strong transcription	Brain Anterior Caudate	brain
14	chr1:246890600-246907600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:246890600-246914000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:246891400-246904200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:246891800-246911600	Strong transcription	Liver	Liver
18	chr1:246892400-246912000	Strong transcription	Dnd41	blood
19	chr1:246892600-246904600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:246892600-246908800	Strong transcription	Fetal Stomach	stomach
21	chr1:246892600-246909200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:246892600-246924400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:246893400-246903800	Strong transcription	A549	lung
24	chr1:246893400-246906800	Strong transcription	Brain Cingulate Gyrus	brain
25	chr1:246893600-246905000	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr1:246893800-246903600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:246893800-246912800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:246894000-246904000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:246894200-246904400	Weak transcription	Psoas Muscle	Psoas
30	chr1:246894400-246909600	Strong transcription	Placenta	Placenta
31	chr1:246894600-246923800	Weak transcription	Pancreas	Pancrea
32	chr1:246895000-246904000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr1:246895000-246904000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:246895000-246904600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:246895000-246906600	Strong transcription	Fetal Intestine Large	intestine
36	chr1:246895000-246907400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:246895000-246909000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:246895000-246909200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr1:246895000-246912000	Weak transcription	Spleen	Spleen
40	chr1:246895000-246942200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr1:246895400-246938600	Weak transcription	Fetal Heart	heart
42	chr1:246896400-246917000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr1:246897400-246909000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:246897400-246909200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:246897600-246909200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:246897600-246912400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:246897800-246907400	Strong transcription	Adipose Nuclei	Adipose
48	chr1:246898000-246904000	Weak transcription	Thymus	Thymus
49	chr1:246899200-246905400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:246899400-246903600	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links