Variant report

Variant	rs34048530
Chromosome Location	chr1:246887019-246887020
allele	A/C
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	TCF12	chr1:246887001-246888510	A549	lung:	n/a	n/a
2	MAX	chr1:246886994-246888634	A549	lung:	n/a	chr1:246887322-246887329 chr1:246887319-246887328
3	MTA3	chr1:246887001-246888461	GM12878	blood:	n/a	n/a
4	SIN3AK20	chr1:246887017-246888465	MCF-7	breast:	n/a	n/a
5	REST	chr1:246886976-246888531	H1-neurons	neurons:	n/a	n/a
6	GTF3C2	chr1:246886928-246887906	K562	blood:	n/a	n/a
7	POLR2A	chr1:246887013-246888193	H1-hESC	embryonic stem cell:	n/a	n/a
8	EP300	chr1:246887012-246887938	SK-N-SH	brain:	n/a	chr1:246887379-246887395 chr1:246887435-246887451 chr1:246887431-246887440
9	MXI1	chr1:246887017-246888846	SK-N-SH	brain:	n/a	n/a
10	CBX3	chr1:246886892-246888564	K562	blood:	n/a	n/a
11	POLR2A	chr1:246887001-246888343	HepG2	liver:	n/a	n/a
12	MAX	chr1:246886993-246888518	ECC-1	luminal epithelium:	n/a	chr1:246887322-246887329 chr1:246887319-246887328
13	MAX	chr1:246887017-246888640	HepG2	liver:	n/a	chr1:246887322-246887329 chr1:246887319-246887328
14	TCF12	chr1:246886953-246888232	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246853163..246855096-chr1:246886538..246888986,3	MCF-7	breast:
2	chr1:246853196..246855742-chr1:246886661..246889205,4	MCF-7	breast:

Variant related genes	Relation type
SCCPDH	TF binding region
ENSG00000235021	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10924813	0.83[AFR][1000 genomes]
rs1127098	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1127149	0.88[ASN][1000 genomes]
rs12121187	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12121214	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12124832	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12128579	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12129386	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12129828	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12735300	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087781	0.82[ASN][1000 genomes]
rs34677128	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35021082	0.82[AMR][1000 genomes]
rs35570407	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35736382	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795469	0.90[ASN][1000 genomes]
rs4078128	0.82[ASN][1000 genomes]
rs41310575	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4926440	0.88[ASN][1000 genomes]
rs4926442	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4926443	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4926444	0.87[ASN][1000 genomes]
rs4926447	0.82[AMR][1000 genomes]
rs4926449	0.88[ASN][1000 genomes]
rs4926450	0.90[ASN][1000 genomes]
rs4926456	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61684731	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61852479	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61852481	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61852482	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6426329	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689579	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697433	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697526	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699332	0.88[ASN][1000 genomes]
rs6701991	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7365254	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7366187	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7410830	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74152239	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7513496	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526237	0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7528002	0.86[ASN][1000 genomes]
rs7550482	0.88[ASN][1000 genomes]
rs9659021	0.90[AMR][1000 genomes];0.81[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
rs34048530	SCCPDH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246886600-246887400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:246886600-246887400	Flanking Active TSS	Dnd41	blood
3	chr1:246886600-246888000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:246886600-246888400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:246886600-246888400	Active TSS	Rectal Mucosa Donor 31	rectum
6	chr1:246886600-246888400	Active TSS	NHLF	lung
7	chr1:246886600-246888600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:246886600-246889000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:246886800-246887200	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr1:246886800-246887200	Flanking Active TSS	Fetal Muscle Trunk	muscle
11	chr1:246886800-246887400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:246886800-246887400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr1:246886800-246887400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:246886800-246887400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:246886800-246887400	Active TSS	Right Atrium	heart
16	chr1:246886800-246887400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr1:246886800-246887600	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr1:246886800-246887800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:246886800-246887800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:246886800-246887800	Active TSS	HepG2	liver
21	chr1:246886800-246888000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:246886800-246888000	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr1:246886800-246888200	Active TSS	Primary T cells from cord blood	blood
24	chr1:246886800-246888200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:246886800-246888200	Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr1:246886800-246888400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
27	chr1:246886800-246888400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr1:246886800-246888400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:246886800-246888400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:246886800-246888400	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr1:246886800-246888400	Active TSS	Aorta	Aorta
32	chr1:246886800-246888400	Active TSS	Brain Anterior Caudate	brain
33	chr1:246886800-246888400	Active TSS	Brain Cingulate Gyrus	brain
34	chr1:246886800-246888400	Active TSS	Brain Germinal Matrix	brain
35	chr1:246886800-246888400	Active TSS	Stomach Smooth Muscle	stomach
36	chr1:246886800-246888400	Active TSS	A549	lung
37	chr1:246886800-246888400	Active TSS	GM12878-XiMat	blood
38	chr1:246886800-246888600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:246886800-246888600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:246886800-246888600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:246886800-246888600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:246886800-246888600	Active TSS	Brain Angular Gyrus	brain
43	chr1:246886800-246888600	Active TSS	Colon Smooth Muscle	Colon
44	chr1:246886800-246888600	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr1:246886800-246888600	Active TSS	Fetal Intestine Large	intestine
46	chr1:246886800-246888600	Active TSS	Fetal Intestine Small	intestine
47	chr1:246886800-246888600	Active TSS	Fetal Stomach	stomach
48	chr1:246886800-246888600	Active TSS	Right Ventricle	heart
49	chr1:246886800-246888800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:246886800-246888800	Active TSS	Brain Substantia Nigra	brain

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