Variant report

Variant	rs34677128
Chromosome Location	chr1:246890158-246890159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246868796..246870534-chr1:246889935..246891767,2	K562	blood:
2	chr1:246862215..246864763-chr1:246888186..246891481,3	K562	blood:
3	chr1:246884666..246886259-chr1:246889523..246891914,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1127098	0.88[ASN][1000 genomes]
rs1127149	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12121187	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12121214	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12124832	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12128579	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12129386	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12129828	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12402095	0.87[ASN][1000 genomes]
rs12403128	0.90[ASN][1000 genomes]
rs12409066	0.87[ASN][1000 genomes]
rs12410595	0.87[ASN][1000 genomes]
rs12735300	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087781	0.82[ASN][1000 genomes]
rs34048530	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35570407	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35736382	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795469	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4078128	0.82[ASN][1000 genomes]
rs41310575	0.88[ASN][1000 genomes]
rs4926440	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4926442	0.87[ASN][1000 genomes]
rs4926443	0.87[ASN][1000 genomes]
rs4926444	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4926449	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4926450	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4926456	0.87[ASN][1000 genomes]
rs61684731	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61852479	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61852481	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61852482	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6426329	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689579	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697433	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697526	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699332	0.88[ASN][1000 genomes]
rs6701991	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7365254	1.00[ASN][1000 genomes]
rs7366187	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7410830	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74152239	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7513496	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526237	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7528002	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7550482	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9659021	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34677128	SCCPDH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246890600	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr1:246888400-246890800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:246888400-246891000	Weak transcription	Aorta	Aorta
4	chr1:246888400-246891600	Weak transcription	Esophagus	oesophagus
5	chr1:246888400-246893400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:246888400-246896000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:246888400-246900000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:246888400-246902000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:246888400-246903800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
11	chr1:246888600-246890200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:246888600-246890200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:246888600-246890200	Enhancers	Placenta	Placenta
14	chr1:246888600-246890400	Weak transcription	Psoas Muscle	Psoas
15	chr1:246888600-246890600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr1:246888600-246890600	Flanking Active TSS	Liver	Liver
17	chr1:246888600-246890600	Enhancers	Hela-S3	cervix
18	chr1:246888600-246890800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:246888600-246890800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:246888600-246891400	Weak transcription	Right Ventricle	heart
21	chr1:246888600-246893400	Weak transcription	Primary B cells from cord blood	blood
22	chr1:246888600-246901400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:246888800-246890200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:246888800-246890200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:246888800-246890200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:246888800-246890200	Weak transcription	Primary T cells from cord blood	blood
28	chr1:246888800-246890200	Weak transcription	Left Ventricle	heart
29	chr1:246888800-246890200	Weak transcription	Thymus	Thymus
30	chr1:246888800-246890200	Weak transcription	HSMMtube	muscle
31	chr1:246888800-246890800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:246888800-246890800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:246888800-246890800	Weak transcription	Ovary	ovary
34	chr1:246888800-246891000	Weak transcription	Gastric	stomach
35	chr1:246888800-246891000	Weak transcription	Spleen	Spleen
36	chr1:246888800-246891200	Weak transcription	Lung	lung
37	chr1:246888800-246891600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:246888800-246892400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:246888800-246897400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:246888800-246904000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:246888800-246904800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:246889000-246890200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:246889000-246890200	Enhancers	Brain Anterior Caudate	brain
44	chr1:246889000-246890200	Weak transcription	Fetal Brain Female	brain
45	chr1:246889000-246890200	Enhancers	Fetal Intestine Large	intestine
46	chr1:246889000-246890200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:246889000-246890200	Weak transcription	GM12878-XiMat	blood
48	chr1:246889000-246890200	Weak transcription	HUVEC	blood vessel
49	chr1:246889000-246890200	Weak transcription	NH-A	brain
50	chr1:246889000-246890200	Weak transcription	Osteobl	bone

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