Variant report

Variant	rs648743
Chromosome Location	chr1:70875779-70875780
allele	C/T
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	NRF1	chr1:70875695-70877205	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:70875699-70878933	H1-hESC	embryonic stem cell:	n/a	n/a
3	CHD1	chr1:70875776-70877997	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:70819015..70821620-chr1:70875663..70878848,3	MCF-7	breast:
2	chr1:70818087..70822177-chr1:70874224..70879265,8	K562	blood:
3	chr1:70818443..70821962-chr1:70874400..70876118,3	MCF-7	breast:
4	chr1:70814842..70821925-chr1:70874223..70879265,8	K562	blood:

Variant related genes	Relation type
CTH	TF binding region
ENSG00000197568	Chromatin interaction
ENSG00000118454	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs4620474	0.81[CEU][hapmap]
rs4650037	0.96[CEU][hapmap];0.89[CHB][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs482843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs487773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs531880	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs540003	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6424385	0.96[CEU][hapmap];0.89[CHB][hapmap]
rs663465	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs828350	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs828351	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs828352	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs998522	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	esv1797324	chr1:70858435-70876569	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	n/a
4	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs648743	CTH	cis	multi-tissue	Pritchard
rs648743	CTH	Cis_1M	lymphoblastoid	RTeQTL
rs648743	CTH	cis	Whole Blood	GTEx
rs648743	CTH	cis	lymphoblastoid	seeQTL
rs648743	HHLA3	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70871600-70875800	Weak transcription	HUVEC	blood vessel
2	chr1:70871800-70875800	Weak transcription	Fetal Lung	lung
3	chr1:70872800-70875800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:70872800-70876000	Weak transcription	Adipose Nuclei	Adipose
5	chr1:70874800-70875800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:70874800-70876200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:70875200-70875800	Enhancers	Liver	Liver
8	chr1:70875400-70875800	Enhancers	Hela-S3	cervix
9	chr1:70875400-70876000	Active TSS	HepG2	liver
10	chr1:70875600-70875800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:70875600-70875800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr1:70875600-70875800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr1:70875600-70875800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:70875600-70875800	Enhancers	Primary B cells from cord blood	blood
15	chr1:70875600-70875800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr1:70875600-70875800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:70875600-70875800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:70875600-70875800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:70875600-70875800	Enhancers	Brain Angular Gyrus	brain
20	chr1:70875600-70875800	Enhancers	Brain Anterior Caudate	brain
21	chr1:70875600-70875800	Enhancers	Brain Hippocampus Middle	brain
22	chr1:70875600-70875800	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr1:70875600-70875800	Enhancers	Fetal Brain Female	brain
24	chr1:70875600-70875800	Enhancers	Rectal Smooth Muscle	rectum
25	chr1:70875600-70875800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr1:70875600-70875800	Enhancers	Stomach Smooth Muscle	stomach
27	chr1:70875600-70875800	Enhancers	A549	lung
28	chr1:70875600-70875800	Enhancers	Dnd41	blood
29	chr1:70875600-70875800	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr1:70875600-70876000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr1:70875600-70876000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr1:70875600-70876400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:70875600-70878000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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