Variant report

Variant	rs3760568
Chromosome Location	chr18:29671721-29671722
allele	A/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	FOXM1	chr18:29671667-29672311	GM12878	blood:	n/a	n/a
2	BCLAF1	chr18:29671581-29672203	GM12878	blood:	n/a	chr18:29671982-29671995 chr18:29671983-29671992
3	MYBL2	chr18:29671544-29672108	HepG2	liver:	n/a	n/a
4	YY1	chr18:29671717-29672449	GM12891	blood:	n/a	chr18:29671982-29671991 chr18:29671985-29671994 chr18:29672227-29672238 chr18:29672372-29672386 chr18:29671976-29671990
5	POLR2A	chr18:29671658-29672498	U87	brain:	n/a	n/a
6	POLR2A	chr18:29671679-29673371	HepG2	liver:	n/a	n/a
7	POLR2A	chr18:29671655-29672460	HUVEC	blood vessel:	n/a	n/a
8	MAX	chr18:29671589-29673739	K562	blood:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
9	POLR2A	chr18:29671577-29673722	Hela-S3	cervix:	n/a	n/a
10	UBTF	chr18:29671525-29673774	K562	blood:	n/a	n/a
11	POLR2A	chr18:29671489-29672893	PANC-1	pancreas:	n/a	n/a
12	STAT1	chr18:29671595-29672831	GM12878	blood:	n/a	chr18:29672294-29672306 chr18:29672425-29672437 chr18:29672579-29672591
13	MAZ	chr18:29671619-29673046	HepG2	liver:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
14	MAFK	chr18:29671481-29672003	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr18:29671585-29673547	GM18526	blood:	n/a	n/a
16	TEAD4	chr18:29671593-29672289	K562	blood:	n/a	n/a
17	CREB1	chr18:29671626-29672900	A549	lung:	n/a	n/a
18	MYC	chr18:29671529-29673824	K562	blood:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
19	CHD2	chr18:29671568-29673542	Hela-S3	cervix:	n/a	chr18:29672248-29672258 chr18:29672637-29672647 chr18:29672437-29672447 chr18:29672425-29672435 chr18:29671773-29671783 chr18:29673301-29673311
20	POLR2A	chr18:29671658-29672040	U87	brain:	n/a	n/a
21	CREB1	chr18:29671593-29672109	ECC-1	luminal epithelium:	n/a	n/a
22	MYC	chr18:29671622-29673802	K562	blood:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
23	REST	chr18:29671472-29672999	HL-60	blood:	n/a	chr18:29672354-29672367 chr18:29671888-29671901
24	GTF2F1	chr18:29671675-29672100	H1-hESC	embryonic stem cell:	n/a	n/a
25	NRF1	chr18:29671500-29672064	GM12878	blood:	n/a	n/a
26	TBP	chr18:29671514-29672001	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr18:29671589-29673553	GM15510	blood:	n/a	n/a
28	POLR2A	chr18:29671457-29673811	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr18:29671639-29673417	GM12878	blood:	n/a	n/a
30	POLR2A	chr18:29671417-29673037	HUVEC	blood vessel:	n/a	n/a
31	CHD2	chr18:29671583-29672915	H1-hESC	embryonic stem cell:	n/a	chr18:29672248-29672258 chr18:29672637-29672647 chr18:29672437-29672447 chr18:29672425-29672435 chr18:29671773-29671783
32	HA-E2F1	chr18:29671449-29673562	MCF-7	breast:	n/a	chr18:29673118-29673125 chr18:29673118-29673125 chr18:29671985-29671994 chr18:29673118-29673125 chr18:29672983-29672998 chr18:29672596-29672605 chr18:29671983-29671993 chr18:29673117-29673129
33	ELF1	chr18:29671623-29672773	K562	blood:	n/a	chr18:29671982-29671991 chr18:29672213-29672222 chr18:29672354-29672366 chr18:29671983-29671995 chr18:29672097-29672109
34	MAX	chr18:29671524-29673420	A549	lung:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
35	UBTF	chr18:29671568-29673750	K562	blood:	n/a	n/a
36	MAX	chr18:29671564-29673379	ECC-1	luminal epithelium:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
37	TAF1	chr18:29671667-29672989	H1-neurons	neurons:	n/a	n/a
38	ARID3A	chr18:29671653-29671722	K562	blood:	n/a	n/a
39	E2F1	chr18:29671625-29673322	Hela-S3	cervix:	n/a	chr18:29673118-29673125 chr18:29673118-29673125 chr18:29671985-29671994 chr18:29673118-29673125 chr18:29672983-29672998 chr18:29672596-29672605 chr18:29671983-29671993 chr18:29673117-29673129
40	TCF12	chr18:29671625-29673537	ECC-1	luminal epithelium:	n/a	n/a
41	HMGN3	chr18:29671627-29673412	K562	blood:	n/a	n/a
42	PAX5	chr18:29671721-29672006	GM12892	blood:	n/a	chr18:29671759-29671777 chr18:29671760-29671779
43	PML	chr18:29671532-29672416	K562	blood:	n/a	n/a
44	MXI1	chr18:29671449-29673532	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr18:29671689-29672947	H1-hESC	embryonic stem cell:	n/a	n/a
46	WRNIP1	chr18:29671600-29671930	GM12878	blood:	n/a	n/a
47	POU2F2	chr18:29671653-29672136	GM12891	blood:	n/a	chr18:29671976-29671988
48	SMARCB1	chr18:29671652-29673390	Hela-S3	cervix:	n/a	n/a
49	TFAP2A	chr18:29671564-29673358	Hela-S3	cervix:	n/a	chr18:29672072-29672080 chr18:29671984-29671995 chr18:29672071-29672079 chr18:29673123-29673135 chr18:29672072-29672080 chr18:29672898-29672910 chr18:29673126-29673134 chr18:29673126-29673134 chr18:29673123-29673135 chr18:29672070-29672081 chr18:29672071-29672079 chr18:29672070-29672081 chr18:29673123-29673135 chr18:29673123-29673135 chr18:29672922-29672937 chr18:29673126-29673134 chr18:29672072-29672080 chr18:29672070-29672081 chr18:29672071-29672079
50	RCOR1	chr18:29671443-29672911	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:29521939..29525237-chr18:29670716..29673913,4	MCF-7	breast:
2	chr18:29598540..29599388-chr18:29671670..29672456,2	Hela-S3	cervix:
3	chr18:29596689..29599956-chr18:29670764..29674475,6	MCF-7	breast:
4	chr18:29670755..29674701-chr18:29702072..29706406,4	K562	blood:
5	chr18:29671504..29673421-chr18:30049351..30052237,2	K562	blood:
6	chr18:29637884..29642506-chr18:29670649..29674281,4	K562	blood:
7	chr18:29597506..29599866-chr18:29670953..29673378,4	MCF-7	breast:
8	chr18:29521618..29525019-chr18:29670361..29672184,4	MCF-7	breast:
9	chr18:29654269..29657288-chr18:29670351..29673351,3	K562	blood:
10	chr18:29521537..29525393-chr18:29670839..29674328,7	K562	blood:
11	chr18:29520857..29524705-chr18:29670705..29674434,7	K562	blood:
12	chr18:29671417..29672347-chr20:42086520..42087354,2	Hela-S3	cervix:

Variant related genes	Relation type
RNF138	TF binding region
ENSG00000238982	TF binding region
ENSG00000263393	Chromatin interaction
ENSG00000263917	Chromatin interaction
ENSG00000141441	Chromatin interaction
ENSG00000134758	Chromatin interaction
ENSG00000101695	Chromatin interaction
ENSG00000153339	Chromatin interaction
ENSG00000124193	Chromatin interaction
ENSG00000214917	Chromatin interaction
ENSG00000263823	Chromatin interaction
ENSG00000265063	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1054667	0.84[GIH][hapmap]
rs11081741	0.82[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.80[EUR][1000 genomes]
rs11081746	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11663563	0.92[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs12458548	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12458837	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12458851	0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12604223	0.82[AMR][1000 genomes]
rs12605137	0.92[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs17718949	1.00[YRI][hapmap]
rs1808891	0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2018380	0.82[CEU][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap]
rs2048245	0.82[CEU][hapmap]
rs3980848	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4799326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4799629	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4799632	0.89[GIH][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62093949	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62093950	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7238559	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9676102	0.96[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs993897	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757673	chr18:29632749-29674992	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2758719	chr18:29632749-29674992	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv909522	chr18:29645496-29674992	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv909523	chr18:29645496-29679922	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1055457	chr18:29654978-29677371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3760568	RNF138	Cis_1M	lymphoblastoid	RTeQTL
rs3760568	RNF138	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29665200-29671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr18:29671200-29672400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr18:29671200-29673800	Active TSS	H1 Cell Line	embryonic stem cell
4	chr18:29671200-29674000	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr18:29671200-29675000	Active TSS	GM12878-XiMat	blood
6	chr18:29671400-29671800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr18:29671400-29671800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr18:29671400-29671800	Flanking Active TSS	Primary B cells from peripheral blood	blood
9	chr18:29671400-29671800	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr18:29671400-29671800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr18:29671400-29671800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr18:29671400-29671800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr18:29671400-29671800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
14	chr18:29671400-29671800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr18:29671400-29671800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr18:29671400-29671800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr18:29671400-29671800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr18:29671400-29671800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr18:29671400-29671800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr18:29671400-29671800	Flanking Active TSS	Liver	Liver
21	chr18:29671400-29671800	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr18:29671400-29671800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr18:29671400-29671800	Flanking Active TSS	Fetal Muscle Leg	muscle
24	chr18:29671400-29671800	Active TSS	Placenta	Placenta
25	chr18:29671400-29671800	Flanking Active TSS	Fetal Stomach	stomach
26	chr18:29671400-29671800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr18:29671400-29671800	Active TSS	Right Atrium	heart
28	chr18:29671400-29671800	Flanking Active TSS	Hela-S3	cervix
29	chr18:29671400-29671800	Flanking Active TSS	HepG2	liver
30	chr18:29671400-29671800	Flanking Active TSS	HUVEC	blood vessel
31	chr18:29671400-29671800	Flanking Active TSS	NHEK	skin
32	chr18:29671400-29671800	Flanking Active TSS	Osteobl	bone
33	chr18:29671400-29672000	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr18:29671400-29672000	Flanking Active TSS	Dnd41	blood
35	chr18:29671400-29672000	Flanking Active TSS	HMEC	breast
36	chr18:29671400-29672200	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr18:29671400-29672200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr18:29671400-29672200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr18:29671400-29672200	Flanking Active TSS	Fetal Thymus	thymus
40	chr18:29671400-29672400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
41	chr18:29671400-29672400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr18:29671400-29672400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr18:29671400-29673400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr18:29671400-29673400	Active TSS	Brain Angular Gyrus	brain
45	chr18:29671400-29673400	Active TSS	Brain Hippocampus Middle	brain
46	chr18:29671400-29673400	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr18:29671400-29673600	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr18:29671400-29673600	Active TSS	Brain Anterior Caudate	brain
49	chr18:29671400-29673600	Active TSS	Brain Cingulate Gyrus	brain
50	chr18:29671400-29673600	Active TSS	Brain Inferior Temporal Lobe	brain

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