Variant report

Variant	rs62093949
Chromosome Location	chr18:29673356-29673357
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	SIN3AK20	chr18:29672284-29673460	SK-N-SH	brain:	n/a	n/a
2	BCLAF1	chr18:29673033-29673725	GM12878	blood:	n/a	n/a
3	POLR2A	chr18:29671679-29673371	HepG2	liver:	n/a	n/a
4	MAX	chr18:29671589-29673739	K562	blood:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
5	POLR2A	chr18:29671577-29673722	Hela-S3	cervix:	n/a	n/a
6	UBTF	chr18:29671525-29673774	K562	blood:	n/a	n/a
7	POLR2A	chr18:29671585-29673547	GM18526	blood:	n/a	n/a
8	MYC	chr18:29671529-29673824	K562	blood:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
9	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
10	MYC	chr18:29671622-29673802	K562	blood:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
11	POLR2A	chr18:29673097-29673794	GM12878	blood:	n/a	n/a
12	POLR2A	chr18:29671589-29673553	GM15510	blood:	n/a	n/a
13	POLR2A	chr18:29671457-29673811	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr18:29671639-29673417	GM12878	blood:	n/a	n/a
15	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
16	MAX	chr18:29671524-29673420	A549	lung:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
17	UBTF	chr18:29671568-29673750	K562	blood:	n/a	n/a
18	MAX	chr18:29671564-29673379	ECC-1	luminal epithelium:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
19	GTF2F1	chr18:29673346-29673393	H1-hESC	embryonic stem cell:	n/a	n/a
20	TCF12	chr18:29671625-29673537	ECC-1	luminal epithelium:	n/a	n/a
21	HMGN3	chr18:29671627-29673412	K562	blood:	n/a	n/a
22	MXI1	chr18:29671449-29673532	Hela-S3	cervix:	n/a	n/a
23	SMARCB1	chr18:29671652-29673390	Hela-S3	cervix:	n/a	n/a
24	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
25	CHD1	chr18:29673337-29673619	GM12878	blood:	n/a	n/a
26	MAZ	chr18:29671509-29673826	K562	blood:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
27	POLR2A	chr18:29671565-29673477	K562	blood:	n/a	n/a
28	BHLHE40	chr18:29671540-29673692	GM12878	blood:	n/a	chr18:29672946-29672962 chr18:29671977-29671993 chr18:29671974-29671990
29	POLR2A	chr18:29671579-29673687	Raji	blood:	n/a	n/a
30	TBL1XR1	chr18:29673218-29673788	GM12878	blood:	n/a	n/a
31	MAX	chr18:29671594-29673681	NB4	blood:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
32	MYC	chr18:29671653-29673464	MCF10A-Er-Src	breast:	n/a	chr18:29672357-29672367 chr18:29672639-29672649 chr18:29672147-29672154 chr18:29672146-29672155
33	POLR2A	chr18:29671438-29673836	K562	blood:	n/a	n/a
34	SIN3AK20	chr18:29672474-29673456	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr18:29671407-29673805	GM12891	blood:	n/a	n/a
36	CHD2	chr18:29671650-29673432	K562	blood:	n/a	chr18:29672248-29672258 chr18:29672637-29672647 chr18:29672437-29672447 chr18:29672425-29672435 chr18:29671773-29671783 chr18:29673301-29673311
37	SIN3AK20	chr18:29672377-29673469	K562	blood:	n/a	n/a
38	POLR2A	chr18:29673166-29673540	GM12891	blood:	n/a	n/a
39	KAP1	chr18:29673293-29673735	U2OS	brain:	n/a	n/a
40	E2F6	chr18:29671606-29673447	H1-hESC	embryonic stem cell:	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
41	ZNF143	chr18:29673314-29673802	K562	blood:	n/a	n/a
42	EP300	chr18:29673337-29673411	GM12878	blood:	n/a	n/a
43	POLR2A	chr18:29671593-29673578	GM12892	blood:	n/a	n/a
44	MXI1	chr18:29671511-29674150	IMR90	lung:	n/a	n/a
45	MTA3	chr18:29673023-29673797	GM12878	blood:	n/a	n/a
46	RCOR1	chr18:29671611-29673939	K562	blood:	n/a	n/a
47	HCFC1	chr18:29671246-29673672	Hela-S3	cervix:	n/a	n/a
48	ZNF263	chr18:29672481-29673652	HEK293-T-REx	kidney:	n/a	chr18:29672513-29672522
49	MAX	chr18:29671627-29673461	GM12878	blood:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649
50	MAX	chr18:29671469-29673374	ECC-1	luminal epithelium:	n/a	chr18:29672357-29672367 chr18:29672147-29672154 chr18:29672146-29672155 chr18:29672639-29672649

No.	Distal block	Cell Line	Cell type
1	chr18:29521939..29525237-chr18:29670716..29673913,4	MCF-7	breast:
2	chr18:29596689..29599956-chr18:29670764..29674475,6	MCF-7	breast:
3	chr18:29672647..29674860-chr18:29703384..29706167,2	MCF-7	breast:
4	chr18:29670755..29674701-chr18:29702072..29706406,4	K562	blood:
5	chr18:29671504..29673421-chr18:30049351..30052237,2	K562	blood:
6	chr18:29521522..29523729-chr18:29672844..29674625,2	MCF-7	breast:
7	chr11:62608032..62609663-chr18:29672517..29674072,2	MCF-7	breast:
8	chr18:29637884..29642506-chr18:29670649..29674281,4	K562	blood:
9	chr18:29597506..29599866-chr18:29670953..29673378,4	MCF-7	breast:
10	chr18:29521537..29525393-chr18:29670839..29674328,7	K562	blood:
11	chr18:29520857..29524705-chr18:29670705..29674434,7	K562	blood:

Variant related genes	Relation type
ENSG00000265008	TF binding region
ENSG00000238982	TF binding region
ENSG00000153339	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000263823	Chromatin interaction
ENSG00000141441	Chromatin interaction
ENSG00000263393	Chromatin interaction
ENSG00000101695	Chromatin interaction
ENSG00000134758	Chromatin interaction
ENSG00000263917	Chromatin interaction
ENSG00000265063	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11081746	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11663563	0.80[AMR][1000 genomes]
rs12458548	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12458837	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12458851	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12604223	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12605137	0.82[AMR][1000 genomes]
rs1808891	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2048245	0.80[AMR][1000 genomes]
rs3760568	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3980848	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4799326	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4799629	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4799632	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62093950	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7238559	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9676102	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs993897	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62093949	RNF138	cis	multi-tissue	Pritchard
rs62093949	RNF138	cis	Esophagus Mucosa	GTEx
rs62093949	RNF138	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29671200-29673800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr18:29671200-29674000	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr18:29671200-29675000	Active TSS	GM12878-XiMat	blood
4	chr18:29671400-29673400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr18:29671400-29673400	Active TSS	Brain Angular Gyrus	brain
6	chr18:29671400-29673400	Active TSS	Brain Hippocampus Middle	brain
7	chr18:29671400-29673400	Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr18:29671400-29673600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr18:29671400-29673600	Active TSS	Brain Anterior Caudate	brain
10	chr18:29671400-29673600	Active TSS	Brain Cingulate Gyrus	brain
11	chr18:29671400-29673600	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr18:29671400-29673600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr18:29671400-29673600	Active TSS	Colon Smooth Muscle	Colon
14	chr18:29671400-29673600	Active TSS	Fetal Brain Male	brain
15	chr18:29671400-29673800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr18:29671400-29673800	Active TSS	Aorta	Aorta
17	chr18:29671400-29673800	Active TSS	Colonic Mucosa	Colon
18	chr18:29671400-29673800	Active TSS	Placenta Amnion	Placenta Amnion
19	chr18:29671400-29673800	Active TSS	Psoas Muscle	Psoas
20	chr18:29671400-29673800	Active TSS	Thymus	Thymus
21	chr18:29671400-29673800	Active TSS	HSMMtube	muscle
22	chr18:29671400-29674000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr18:29671400-29674000	Active TSS	H9 Cell Line	embryonic stem cell
24	chr18:29671400-29674000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr18:29671400-29674000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr18:29671400-29674000	Active TSS	Fetal Intestine Small	intestine
27	chr18:29671400-29674000	Active TSS	Right Ventricle	heart
28	chr18:29671400-29674200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr18:29671400-29674200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr18:29671400-29674200	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr18:29671400-29674200	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr18:29671400-29674200	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr18:29671400-29674200	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr18:29671400-29674200	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr18:29671400-29674200	Active TSS	A549	lung
36	chr18:29671400-29674200	Active TSS	NH-A	brain
37	chr18:29671400-29674200	Active TSS	NHDF-Ad	bronchial
38	chr18:29671400-29674400	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr18:29671400-29674400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr18:29671400-29674800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr18:29671600-29673400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr18:29671600-29673400	Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr18:29671600-29673400	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr18:29671600-29673400	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr18:29671600-29673400	Active TSS	Spleen	Spleen
46	chr18:29671600-29673600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr18:29671600-29673600	Active TSS	Primary T cells from cord blood	blood
48	chr18:29671600-29673600	Active TSS	Brain Substantia Nigra	brain
49	chr18:29671600-29673600	Active TSS	Fetal Kidney	kidney
50	chr18:29671600-29673600	Active TSS	Left Ventricle	heart

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