Variant report

Variant	rs9659021
Chromosome Location	chr1:246896500-246896501
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246892836..246895374-chr1:246896028..246898230,2	K562	blood:
2	chr1:246817628..246820326-chr1:246894643..246896981,2	MCF-7	breast:
3	chr1:246886185..246892082-chr1:246893127..246900077,11	K562	blood:

Variant related genes	Relation type
ENSG00000143653	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1127098	0.89[ASN][1000 genomes]
rs1127149	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12121187	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12121214	0.86[AMR][1000 genomes]
rs12124832	0.85[AMR][1000 genomes]
rs12128579	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12129386	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12129828	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12402095	0.85[ASN][1000 genomes]
rs12403128	0.87[ASN][1000 genomes]
rs12409066	0.85[ASN][1000 genomes]
rs12410595	0.85[ASN][1000 genomes]
rs12735300	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3087781	0.80[ASN][1000 genomes]
rs34048530	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34677128	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35570407	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35736382	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3795469	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4078128	0.80[ASN][1000 genomes]
rs41310575	0.89[ASN][1000 genomes]
rs4926440	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4926442	0.85[ASN][1000 genomes]
rs4926443	0.85[ASN][1000 genomes]
rs4926444	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4926449	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4926450	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4926456	0.85[ASN][1000 genomes]
rs61684731	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61852479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61852481	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61852482	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6426329	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6689579	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6697433	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6697526	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6699332	0.86[ASN][1000 genomes]
rs6701991	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7365254	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7366187	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7410830	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74152239	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7513496	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7526237	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7528002	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7550482	0.88[AMR][1000 genomes];0.89[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9659021	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	chr1:246888400-246900000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:246888400-246902000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:246888400-246903800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
5	chr1:246888600-246901400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:246888800-246897400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:246888800-246904000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:246888800-246904800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:246889000-246929000	Weak transcription	Stomach Mucosa	stomach
11	chr1:246889200-246900600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:246889600-246907000	Strong transcription	Fetal Muscle Trunk	muscle
13	chr1:246890200-246897800	Strong transcription	Fetal Lung	lung
14	chr1:246890200-246898200	Strong transcription	Primary T cells from cord blood	blood
15	chr1:246890200-246898200	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:246890200-246901000	Strong transcription	Osteobl	bone
17	chr1:246890200-246901200	Strong transcription	Fetal Brain Female	brain
18	chr1:246890200-246901200	Strong transcription	HSMMtube	muscle
19	chr1:246890200-246901600	Strong transcription	Fetal Thymus	thymus
20	chr1:246890200-246901600	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:246890200-246902800	Strong transcription	Left Ventricle	heart
22	chr1:246890200-246905000	Strong transcription	Duodenum Mucosa	Duodenum
23	chr1:246890200-246906600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:246890200-246913200	Strong transcription	Fetal Muscle Leg	muscle
25	chr1:246890400-246896600	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr1:246890400-246896800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:246890400-246907400	Strong transcription	Stomach Smooth Muscle	stomach
28	chr1:246890400-246909000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:246890600-246905000	Strong transcription	Brain Anterior Caudate	brain
30	chr1:246890600-246907600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:246890600-246914000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:246890800-246897000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:246890800-246897400	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:246891400-246896800	Strong transcription	Adipose Nuclei	Adipose
35	chr1:246891400-246904200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:246891800-246911600	Strong transcription	Liver	Liver
37	chr1:246892200-246897000	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr1:246892400-246912000	Strong transcription	Dnd41	blood
39	chr1:246892600-246897400	Strong transcription	Primary hematopoietic stem cells	blood
40	chr1:246892600-246900800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:246892600-246904600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:246892600-246908800	Strong transcription	Fetal Stomach	stomach
43	chr1:246892600-246909200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:246892600-246924400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:246893200-246900800	Strong transcription	HSMM	muscle
46	chr1:246893400-246897600	Strong transcription	Brain Germinal Matrix	brain
47	chr1:246893400-246903800	Strong transcription	A549	lung
48	chr1:246893400-246906800	Strong transcription	Brain Cingulate Gyrus	brain
49	chr1:246893600-246905000	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr1:246893800-246897400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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