Variant report

Variant	rs12409066
Chromosome Location	chr1:246947549-246947550
allele	C/G
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	POLR2A	chr1:246947536-246947554	K562	blood:	n/a	n/a
2	MAX	chr1:246947451-246948343	K562	blood:	n/a	chr1:246948130-246948140 chr1:246948123-246948139 chr1:246947801-246947808

No.	Distal block	Cell Line	Cell type
1	chr1:246941244..246944008-chr1:246946969..246949951,3	MCF-7	breast:
2	chr1:246939030..246940776-chr1:246947263..246949787,2	MCF-7	breast:
3	chr1:246946643..246948588-chr1:247104112..247106785,2	K562	blood:
4	chr1:246947185..246952305-chr1:246952338..246955724,5	K562	blood:

Variant related genes	Relation type
ENSG00000227953	TF binding region
KIF28P	TF binding region
ENSG00000227953	Chromatin interaction
ENSG00000223519	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1127098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1127149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12034911	0.89[EUR][1000 genomes]
rs12121187	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12128579	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12129386	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs12129828	0.87[ASN][1000 genomes]
rs12402095	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403128	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12407065	0.92[EUR][1000 genomes]
rs12410595	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12735300	0.87[ASN][1000 genomes]
rs3087781	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34048530	0.87[ASN][1000 genomes]
rs34677128	0.87[ASN][1000 genomes]
rs35021082	0.87[AMR][1000 genomes]
rs35570407	0.87[ASN][1000 genomes]
rs35736382	0.87[ASN][1000 genomes]
rs3795469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4078128	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41310575	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4926440	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4926442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4926443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4926444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4926447	0.87[AMR][1000 genomes]
rs4926449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4926450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4926456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61684731	0.88[ASN][1000 genomes]
rs61852479	0.87[ASN][1000 genomes]
rs61852481	0.88[ASN][1000 genomes]
rs61852482	0.88[ASN][1000 genomes]
rs6426329	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6668806	1.00[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs6682900	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6689579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6697433	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6697526	0.87[ASN][1000 genomes]
rs6699332	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6701991	0.87[ASN][1000 genomes]
rs72475077	0.82[EUR][1000 genomes]
rs7365254	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7366187	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs7410830	0.85[ASN][1000 genomes]
rs74152239	0.93[ASN][1000 genomes]
rs7513496	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7526237	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7528002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7550482	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7551836	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9659021	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
10	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
11	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
12	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
13	nsv873423	chr1:246923861-246978504	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv549545	chr1:246936353-246963019	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	esv3408268	chr1:246944429-246948627	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	esv1841827	chr1:246944502-246954313	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	esv3491345	chr1:246945629-246947627	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	esv3491346	chr1:246945629-246947627	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12409066	SCCPDH	Cis_1M	lymphoblastoid	RTeQTL
rs12409066	CGI-49	cis	multi-tissue	Pritchard
rs12409066	SCCPDH	cis	multi-tissue	Pritchard

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:246925200-246952200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:246932400-246952000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:246932600-246948000	Strong transcription	Liver	Liver
5	chr1:246932600-246948600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:246932600-246948600	Weak transcription	Esophagus	oesophagus
7	chr1:246932800-246948800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:246932800-246952400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:246932800-246956400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:246940200-246947600	Weak transcription	HUVEC	blood vessel
11	chr1:246940200-246948800	Weak transcription	Fetal Brain Male	brain
12	chr1:246940400-246949000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:246940600-246948600	Weak transcription	Brain Angular Gyrus	brain
14	chr1:246940600-246948800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:246940600-246948800	Weak transcription	Fetal Kidney	kidney
16	chr1:246940800-246948000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:246940800-246951600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:246940800-246951600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:246941200-246948200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:246941200-246952600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:246941600-246948800	Weak transcription	Colonic Mucosa	Colon
22	chr1:246941600-246948800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:246941600-246952200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:246942200-246949000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:246942800-246952200	Weak transcription	Fetal Brain Female	brain
26	chr1:246943000-246948000	Enhancers	Primary hematopoietic stem cells	blood
27	chr1:246943400-246952000	Weak transcription	Brain Anterior Caudate	brain
28	chr1:246944200-246947800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:246944400-246948800	Weak transcription	Gastric	stomach
30	chr1:246944600-246947800	Genic enhancers	Fetal Muscle Trunk	muscle
31	chr1:246944600-246952200	Weak transcription	NH-A	brain
32	chr1:246944800-246947800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:246944800-246948200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:246944800-246952000	Weak transcription	Fetal Intestine Large	intestine
35	chr1:246944800-246952200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:246945000-246948800	Weak transcription	Brain Germinal Matrix	brain
37	chr1:246945200-246948000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:246945200-246949400	Enhancers	Fetal Muscle Leg	muscle
39	chr1:246945800-246947800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:246945800-246948000	Enhancers	Primary T cells from cord blood	blood
41	chr1:246945800-246949000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr1:246945800-246956400	Weak transcription	A549	lung
43	chr1:246946000-246947800	Weak transcription	NHLF	lung
44	chr1:246946000-246948800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:246946200-246947600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr1:246946200-246947600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:246946200-246947800	Weak transcription	Primary B cells from cord blood	blood
48	chr1:246946200-246947800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:246946200-246947800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:246946200-246947800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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