Variant report

Variant	rs2039415
Chromosome Location	chr1:160854445-160854446
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	SMC3	chr1:160854235-160854830	SK-N-SH	brain:	n/a	n/a
2	ZNF143	chr1:160854435-160854788	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr1:160854409-160854798	HepG2	liver:	n/a	n/a
4	RAD21	chr1:160854422-160854793	Hela-S3	cervix:	n/a	n/a
5	ELF1	chr1:160854264-160854673	GM12878	blood:	n/a	chr1:160854558-160854567 chr1:160854555-160854568 chr1:160854557-160854568 chr1:160854557-160854568
6	CTCF	chr1:160854436-160854844	K562	blood:	n/a	n/a
7	ELF1	chr1:160854384-160854691	HepG2	liver:	n/a	chr1:160854558-160854567 chr1:160854555-160854568 chr1:160854557-160854568 chr1:160854557-160854568
8	ELF1	chr1:160854316-160854751	K562	blood:	n/a	chr1:160854558-160854567 chr1:160854555-160854568 chr1:160854557-160854568 chr1:160854557-160854568
9	MAX	chr1:160854407-160854723	K562	blood:	n/a	n/a
10	SMC3	chr1:160854431-160854809	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr1:160854380-160854530	A549	lung:	n/a	n/a
12	ELF1	chr1:160854383-160854606	K562	blood:	n/a	chr1:160854558-160854567 chr1:160854555-160854568 chr1:160854557-160854568 chr1:160854557-160854568
13	CTCF	chr1:160854400-160854550	HCM	heart:	n/a	n/a
14	CTCF	chr1:160854443-160854739	K562	blood:	n/a	n/a
15	ELF1	chr1:160854315-160854767	HepG2	liver:	n/a	chr1:160854558-160854567 chr1:160854555-160854568 chr1:160854557-160854568 chr1:160854557-160854568
16	FOSL2	chr1:160854439-160854680	HepG2	liver:	n/a	n/a
17	RAD21	chr1:160854361-160854875	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr1:160854246-160854930	SK-N-SH	brain:	n/a	n/a
19	CTCF	chr1:160854407-160854785	H1-hESC	embryonic stem cell:	n/a	n/a
20	RAD21	chr1:160854431-160854765	HepG2	liver:	n/a	n/a
21	ELF1	chr1:160854430-160854724	MCF-7	breast:	n/a	chr1:160854558-160854567 chr1:160854555-160854568 chr1:160854557-160854568 chr1:160854557-160854568

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160850691..160852389-chr1:160852476..160855044,2	MCF-7	breast:

Variant related genes	Relation type
ITLN1	TF binding region
ENSG00000179914	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10797087	0.87[EUR][1000 genomes]
rs10908808	0.92[EUR][1000 genomes]
rs10908809	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908810	0.85[EUR][1000 genomes]
rs10908811	0.87[EUR][1000 genomes]
rs10908812	0.87[EUR][1000 genomes]
rs11265504	0.86[AMR][1000 genomes]
rs11265510	0.92[CEU][hapmap];0.81[MEX][hapmap];0.88[EUR][1000 genomes]
rs11265514	0.85[EUR][1000 genomes]
rs11265516	0.87[EUR][1000 genomes]
rs11265519	0.87[EUR][1000 genomes]
rs11578752	0.83[EUR][1000 genomes]
rs11587040	0.88[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap]
rs12125065	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12126310	0.85[MEX][hapmap]
rs12135639	0.84[EUR][1000 genomes]
rs12409609	0.91[EUR][1000 genomes]
rs12740520	0.80[EUR][1000 genomes]
rs1333062	0.91[EUR][1000 genomes]
rs17387157	0.92[EUR][1000 genomes]
rs1810924	0.86[EUR][1000 genomes]
rs1855186	0.88[CEU][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.80[EUR][1000 genomes]
rs1855187	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs1930596	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1930598	0.80[EUR][1000 genomes]
rs2184064	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2184068	0.82[AMR][1000 genomes]
rs2225591	0.87[EUR][1000 genomes]
rs2236515	0.96[CEU][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2274905	0.96[CEU][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes]
rs2274907	0.96[CEU][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2274908	0.96[CEU][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2274909	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2274910	0.96[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2297559	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34067571	0.87[EUR][1000 genomes]
rs3766356	0.96[CEU][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes]
rs3766357	0.92[EUR][1000 genomes]
rs3766359	0.92[EUR][1000 genomes]
rs3818724	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3820094	0.96[CEU][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3829790	0.81[MEX][hapmap]
rs3953095	0.81[EUR][1000 genomes]
rs4017459	0.86[AMR][1000 genomes]
rs4656277	0.81[EUR][1000 genomes]
rs4656949	0.86[AMR][1000 genomes]
rs4656951	0.86[EUR][1000 genomes]
rs4656953	0.91[EUR][1000 genomes]
rs4656955	0.92[EUR][1000 genomes]
rs4656956	0.96[CEU][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4656957	0.96[CEU][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4656958	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656959	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4656971	0.81[MEX][hapmap]
rs6427550	0.92[EUR][1000 genomes]
rs6427551	0.92[EUR][1000 genomes]
rs6427552	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6427553	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6658416	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6667400	0.87[EUR][1000 genomes]
rs6671490	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6691868	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6694415	0.88[EUR][1000 genomes]
rs6703406	0.92[EUR][1000 genomes]
rs6704490	0.87[EUR][1000 genomes]
rs7411035	1.00[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7414826	0.88[EUR][1000 genomes]
rs7516660	0.88[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap]
rs7524351	0.92[EUR][1000 genomes]
rs7532133	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7551697	0.87[EUR][1000 genomes]
rs869167	0.81[AMR][1000 genomes]
rs914793	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	esv3430322	chr1:160851829-160920480	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2039415	SMG5	cis	cerebellum	SCAN
rs2039415	RP11-312J18.6	cis	Thyroid	GTEx
rs2039415	LMNA	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160849200-160855400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:160851000-160855400	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr1:160852400-160855000	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr1:160852800-160855000	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr1:160853600-160854600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr1:160853600-160858800	Weak transcription	Gastric	stomach
7	chr1:160853800-160854600	Enhancers	Spleen	Spleen
8	chr1:160854200-160854600	Active TSS	Fetal Intestine Small	intestine
9	chr1:160854200-160854600	Enhancers	Lung	lung
10	chr1:160854200-160855000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:160854400-160854600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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