Variant report

Variant	rs6426329
Chromosome Location	chr1:246892050-246892051
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246890586..246893581-chr1:246920009..246921935,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1127098	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1127149	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs12121187	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12121214	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12124832	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12128579	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12129386	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12129828	0.96[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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12410595	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12735300	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087781	0.82[ASN][1000 genomes]
rs34048530	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34677128	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35021082	0.85[AMR][1000 genomes]
rs35570407	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35736382	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795469	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4078128	0.82[ASN][1000 genomes]
rs41310575	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4926440	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs4926442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4926443	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4926444	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4926447	0.86[AMR][1000 genomes]
rs4926449	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs4926450	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4926456	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61684731	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61852479	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61852481	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61852482	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6689579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697526	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699332	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6701991	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7365254	1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7366187	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7410830	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74152239	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7513496	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526237	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7528002	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7550482	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs9659021	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9662346	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6426329	SCCPDH	Cis_1M	lymphoblastoid	RTeQTL
rs6426329	SCCPDH	cis	Thyroid	GTEx
rs6426329	CGI-49	cis	multi-tissue	Pritchard
rs6426329	SCCPDH	cis	multi-tissue	Pritchard
rs6426329	SCCPDH	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246893400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:246888400-246896000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:246888400-246900000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:246888400-246902000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:246888400-246903800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
7	chr1:246888600-246893400	Weak transcription	Primary B cells from cord blood	blood
8	chr1:246888600-246901400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:246888800-246892400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:246888800-246897400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:246888800-246904000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:246888800-246904800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:246889000-246893400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:246889000-246893400	Weak transcription	A549	lung
16	chr1:246889000-246929000	Weak transcription	Stomach Mucosa	stomach
17	chr1:246889200-246900600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:246889400-246892200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:246889400-246892400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:246889400-246893600	Weak transcription	Fetal Brain Male	brain
21	chr1:246889400-246894000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:246889600-246907000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:246889800-246892400	Strong transcription	HSMM	muscle
24	chr1:246890000-246894600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:246890000-246895000	Strong transcription	Fetal Kidney	kidney
26	chr1:246890200-246892200	Strong transcription	Thymus	Thymus
27	chr1:246890200-246892200	ZNF genes & repeats	K562	blood
28	chr1:246890200-246892400	ZNF genes & repeats	Dnd41	blood
29	chr1:246890200-246892400	ZNF genes & repeats	GM12878-XiMat	blood
30	chr1:246890200-246892600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:246890200-246892600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:246890200-246894000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
33	chr1:246890200-246895000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr1:246890200-246895000	Strong transcription	HUVEC	blood vessel
35	chr1:246890200-246895400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:246890200-246896400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:246890200-246896400	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr1:246890200-246897800	Strong transcription	Fetal Lung	lung
39	chr1:246890200-246898200	Strong transcription	Primary T cells from cord blood	blood
40	chr1:246890200-246898200	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:246890200-246901000	Strong transcription	Osteobl	bone
42	chr1:246890200-246901200	Strong transcription	Fetal Brain Female	brain
43	chr1:246890200-246901200	Strong transcription	HSMMtube	muscle
44	chr1:246890200-246901600	Strong transcription	Fetal Thymus	thymus
45	chr1:246890200-246901600	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:246890200-246902800	Strong transcription	Left Ventricle	heart
47	chr1:246890200-246905000	Strong transcription	Duodenum Mucosa	Duodenum
48	chr1:246890200-246906600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:246890200-246913200	Strong transcription	Fetal Muscle Leg	muscle
50	chr1:246890400-246894200	Strong transcription	Psoas Muscle	Psoas

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