Variant report

Variant	rs12408458
Chromosome Location	chr1:154186918-154186919
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	ARID3A	chr1:154186892-154187318	HepG2	liver:	n/a	n/a
2	CEBPB	chr1:154186833-154187076	IMR90	lung:	n/a	n/a
3	POLR2A	chr1:154186769-154187666	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:154186750-154187037	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr1:154186630-154187183	K562	blood:	n/a	n/a
6	POLR2A	chr1:154186796-154187146	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154178712..154180249-chr1:154186169..154187712,2	MCF-7	breast:
2	chr1:154149113..154161877-chr1:154185436..154196776,24	K562	blood:
3	chr1:154179575..154184047-chr1:154184381..154189147,7	K562	blood:

Variant related genes	Relation type
C1orf43	TF binding region
ENSG00000143549	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000163263	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10797067	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11265040	0.83[MKK][hapmap]
rs11265122	0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap]
rs11265299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12026475	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1212352	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12405309	0.86[JPT][hapmap]
rs2879788	0.81[EUR][1000 genomes]
rs3828076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4240871	0.81[EUR][1000 genomes]
rs4521985	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap]
rs4845363	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs4845597	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs4845600	0.90[CHD][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap]
rs4845601	0.91[CHD][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap]
rs6659053	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs6664278	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs6667928	0.91[CHD][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap]
rs6671166	0.86[JPT][hapmap]
rs6678826	0.91[CHD][hapmap];0.86[JPT][hapmap];0.88[MKK][hapmap]
rs6719	0.82[EUR][1000 genomes]
rs7535778	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs7551128	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9803857	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12408458	SPRR2D	cis	parietal	SCAN
rs12408458	SCARNA4	cis	cerebellum	SCAN
rs12408458	UBAP2L	Cis_1M	lymphoblastoid	RTeQTL
rs12408458	C1orf43	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154172200-154190000	Weak transcription	Fetal Heart	heart
2	chr1:154177000-154191000	Strong transcription	Fetal Stomach	stomach
3	chr1:154177000-154192000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:154177200-154187200	Strong transcription	Brain Hippocampus Middle	brain
5	chr1:154177200-154187400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:154177200-154187600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:154177200-154190200	Strong transcription	Primary T cells from cord blood	blood
8	chr1:154177400-154190400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:154177600-154187000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:154177600-154187000	Strong transcription	Adipose Nuclei	Adipose
11	chr1:154177600-154187000	Strong transcription	Fetal Brain Female	brain
12	chr1:154177600-154187200	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:154177600-154187400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:154177600-154187400	Strong transcription	Fetal Thymus	thymus
15	chr1:154177600-154191400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:154177800-154187200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:154177800-154187200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr1:154177800-154187200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:154177800-154187200	Strong transcription	Brain Substantia Nigra	brain
20	chr1:154177800-154187200	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr1:154177800-154187200	Strong transcription	Stomach Smooth Muscle	stomach
22	chr1:154177800-154187400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:154177800-154187400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:154177800-154187400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:154177800-154187400	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:154177800-154187400	Strong transcription	Fetal Intestine Large	intestine
27	chr1:154177800-154187600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:154177800-154188000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr1:154177800-154190400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:154177800-154190600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:154177800-154190600	Strong transcription	Fetal Intestine Small	intestine
32	chr1:154177800-154191000	Strong transcription	Fetal Muscle Leg	muscle
33	chr1:154177800-154191400	Strong transcription	Placenta	Placenta
34	chr1:154178000-154187200	Strong transcription	Brain Anterior Caudate	brain
35	chr1:154178000-154189800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:154178200-154189200	Strong transcription	Lung	lung
37	chr1:154178200-154191400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:154178400-154187000	Strong transcription	Ovary	ovary
39	chr1:154178400-154187200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:154178400-154187200	Strong transcription	Primary B cells from cord blood	blood
41	chr1:154178400-154187200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr1:154178400-154187200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:154178400-154187200	Strong transcription	Fetal Lung	lung
44	chr1:154178400-154187200	Strong transcription	Rectal Smooth Muscle	rectum
45	chr1:154178400-154187400	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr1:154178400-154187400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:154178400-154187400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:154178400-154187400	Strong transcription	Dnd41	blood
49	chr1:154178400-154187600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:154178400-154187600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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