Variant report

Variant	rs4942830
Chromosome Location	chr13:50019376-50019377
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:156)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:156 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:50017621-50019784	GM12878	blood:	n/a	n/a
2	FOS	chr13:50018949-50019484	MCF10A-Er-Src	breast:	n/a	n/a
3	RUNX3	chr13:50017513-50019603	GM12878	blood:	n/a	chr13:50018257-50018274
4	BHLHE40	chr13:50017907-50019581	K562	blood:	n/a	n/a
5	TBP	chr13:50017240-50019673	GM12878	blood:	n/a	n/a
6	SPI1	chr13:50019087-50019460	GM12891	blood:	n/a	n/a
7	BHLHE40	chr13:50019165-50019509	A549	lung:	n/a	n/a
8	POLR2A	chr13:50019215-50019491	PFSK-1	brain:	n/a	n/a
9	MAX	chr13:50017930-50019585	Hela-S3	cervix:	n/a	n/a
10	CHD2	chr13:50017490-50019597	GM12878	blood:	n/a	n/a
11	POLR2A	chr13:50017492-50019530	HepG2	liver:	n/a	n/a
12	POLR2A	chr13:50017564-50019513	IMR90	lung:	n/a	n/a
13	POLR2A	chr13:50019359-50019491	K562	blood:	n/a	n/a
14	POLR2A	chr13:50017857-50019527	K562	blood:	n/a	n/a
15	RUNX3	chr13:50017480-50019559	GM12878	blood:	n/a	chr13:50018257-50018274
16	MXI1	chr13:50019161-50019492	H1-hESC	embryonic stem cell:	n/a	n/a
17	EBF1	chr13:50018039-50019575	GM12878	blood:	n/a	n/a
18	RCOR1	chr13:50017867-50019467	Hela-S3	cervix:	n/a	n/a
19	SMARCC1	chr13:50017679-50019558	Hela-S3	cervix:	n/a	n/a
20	MXI1	chr13:50017873-50019492	HepG2	liver:	n/a	n/a
21	TBP	chr13:50017619-50019847	K562	blood:	n/a	n/a
22	MYC	chr13:50018928-50019655	MCF10A-Er-Src	breast:	n/a	n/a
23	MAX	chr13:50017786-50019644	ECC-1	luminal epithelium:	n/a	n/a
24	RAD21	chr13:50018832-50019491	IMR90	lung:	n/a	n/a
25	POLR2A	chr13:50019113-50019471	GM12878	blood:	n/a	n/a
26	GATA1	chr13:50017911-50019700	PBDE	blood:	n/a	chr13:50019464-50019474
27	POLR2A	chr13:50017323-50019634	GM12878	blood:	n/a	n/a
28	GTF2F1	chr13:50018924-50019475	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr13:50017479-50019462	GM19193	blood:	n/a	n/a
30	MAX	chr13:50019144-50019429	HepG2	liver:	n/a	n/a
31	POLR2A	chr13:50017422-50019449	SK-N-MC	brain:	n/a	n/a
32	STAT1	chr13:50017815-50019651	GM12878	blood:	n/a	n/a
33	UBTF	chr13:50018093-50019611	K562	blood:	n/a	n/a
34	USF2	chr13:50017986-50019618	GM12878	blood:	n/a	chr13:50019338-50019349
35	RCOR1	chr13:50017840-50019525	GM12878	blood:	n/a	n/a
36	MTA3	chr13:50017255-50019599	GM12878	blood:	n/a	n/a
37	POLR2A	chr13:50019172-50019483	K562	blood:	n/a	n/a
38	POLR2A	chr13:50017422-50019504	GM12891	blood:	n/a	n/a
39	CHD2	chr13:50017622-50019541	Hela-S3	cervix:	n/a	n/a
40	EP300	chr13:50019147-50019624	GM12878	blood:	n/a	chr13:50019561-50019575
41	POLR2A	chr13:50018381-50019903	K562	blood:	n/a	n/a
42	RELA	chr13:50017253-50019557	GM19099	blood:	n/a	n/a
43	SMC3	chr13:50017722-50019547	GM12878	blood:	n/a	chr13:50018095-50018109
44	USF1	chr13:50019075-50019574	ECC-1	luminal epithelium:	n/a	n/a
45	ARID3A	chr13:50018824-50019531	K562	blood:	n/a	n/a
46	RELA	chr13:50017498-50019558	GM10847	blood:	n/a	n/a
47	MYC	chr13:50018941-50019617	K562	blood:	n/a	n/a
48	YY1	chr13:50019106-50019421	GM12878	blood:	n/a	n/a
49	POLR2A	chr13:50017475-50019583	HL-60	blood:	n/a	n/a
50	SIN3A	chr13:50017866-50019402	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:49668884..49671428-chr13:50017958..50020169,2	MCF-7	breast:
2	chr13:49820702..49823407-chr13:50017509..50020339,3	MCF-7	breast:
3	chr13:50016715..50020360-chr13:50068508..50074036,7	MCF-7	breast:
4	chr13:49820441..49822930-chr13:50018500..50020473,2	K562	blood:
5	chr13:50016508..50019619-chr13:50158297..50162493,5	MCF-7	breast:
6	chr13:50016483..50020444-chr13:50068529..50072853,4	MCF-7	breast:
7	chr13:50016992..50019784-chr13:50159235..50161344,2	K562	blood:
8	chr1:36554087..36554720-chr13:50018951..50019561,2	NB4	blood:
9	chr13:50016440..50019751-chr13:50141127..50144444,4	MCF-7	breast:

No data

Variant related genes	Relation type
CAB39L	TF binding region
ENSG00000102543	Chromatin interaction
ENSG00000199788	Chromatin interaction
ENSG00000136144	Chromatin interaction
ENSG00000116863	Chromatin interaction
ENSG00000136147	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11619265	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12429813	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1322787	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1358991	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1409017	0.84[EUR][1000 genomes]
rs1543513	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17073051	0.80[CEU][hapmap]
rs1980795	0.80[ASW][hapmap]
rs2038638	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2057414	0.96[CEU][hapmap];0.92[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2057416	0.84[EUR][1000 genomes]
rs2077848	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407691	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35980977	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3764089	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4340215	0.83[MEX][hapmap];0.82[TSI][hapmap]
rs4430650	0.82[MEX][hapmap]
rs4941643	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4942833	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs61959992	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6561526	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6561533	0.81[CEU][hapmap]
rs7139494	0.80[CEU][hapmap]
rs721457	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7317772	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7327520	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7987940	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7991226	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7995283	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7997737	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9316454	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9526563	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535244	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535247	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv430558	chr13:49914393-50059354	Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv430559	chr13:49930369-50059354	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430560	chr13:49930643-50059354	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv430562	chr13:49930643-50067246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv430561	chr13:49930643-50089844	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv430564	chr13:49945247-50059354	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv430566	chr13:49945247-50089844	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv430571	chr13:49961137-50059354	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv430570	chr13:49961137-50089844	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv1807924	chr13:49991885-50036730	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv1796315	chr13:49992988-50031868	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv523648	chr13:50005444-50086266	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv561613	chr13:50013622-50086266	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv900070	chr13:50013622-50087142	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4942830	ENSG00000136169	cis	multi-tissue	Pritchard
rs4942830	CAB39L	cis	cerebellum	SCAN
rs4942830	SETDB2	cis	cerebellum	SCAN
rs4942830	RCBTB1	cis	multi-tissue	Pritchard
rs4942830	PHF11	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50016800-50020000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:50017000-50019400	Active TSS	H1 Cell Line	embryonic stem cell
3	chr13:50017000-50019400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr13:50017000-50019600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr13:50017000-50019800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr13:50017000-50019800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr13:50017000-50019800	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr13:50017000-50019800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr13:50017000-50019800	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr13:50017000-50019800	Active TSS	Fetal Intestine Large	intestine
11	chr13:50017000-50019800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr13:50017000-50019800	Active TSS	A549	lung
13	chr13:50017000-50020000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr13:50017000-50020000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr13:50017000-50020000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr13:50017000-50022000	Active TSS	NHLF	lung
17	chr13:50017200-50019400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr13:50017200-50019400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr13:50017200-50019600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr13:50017200-50019600	Active TSS	H9 Cell Line	embryonic stem cell
21	chr13:50017200-50019600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr13:50017200-50019600	Active TSS	Aorta	Aorta
23	chr13:50017200-50019600	Active TSS	Ovary	ovary
24	chr13:50017200-50019600	Active TSS	Stomach Mucosa	stomach
25	chr13:50017200-50019600	Active TSS	HSMM	muscle
26	chr13:50017200-50019600	Active TSS	NHDF-Ad	bronchial
27	chr13:50017200-50019800	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr13:50017200-50019800	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr13:50017200-50019800	Active TSS	Right Atrium	heart
30	chr13:50017200-50020000	Active TSS	Right Ventricle	heart
31	chr13:50017200-50020000	Active TSS	GM12878-XiMat	blood
32	chr13:50017200-50020800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr13:50017200-50022200	Active TSS	K562	blood
34	chr13:50017200-50022400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr13:50017400-50019400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr13:50017400-50019400	Active TSS	Esophagus	oesophagus
37	chr13:50017400-50019400	Active TSS	Gastric	stomach
38	chr13:50017400-50019400	Active TSS	Lung	lung
39	chr13:50017400-50019600	Active TSS	Fetal Kidney	kidney
40	chr13:50017400-50019600	Active TSS	Placenta	Placenta
41	chr13:50017400-50019600	Active TSS	Left Ventricle	heart
42	chr13:50017400-50019800	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr13:50017400-50019800	Active TSS	Brain Hippocampus Middle	brain
44	chr13:50017400-50019800	Active TSS	Colon Smooth Muscle	Colon
45	chr13:50017400-50020000	Active TSS	NHEK	skin
46	chr13:50017400-50020200	Active TSS	Pancreas	Pancrea
47	chr13:50017400-50020200	Active TSS	HMEC	breast
48	chr13:50017400-50020800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr13:50017600-50019400	Active TSS	Small Intestine	intestine
50	chr13:50017600-50019400	Active TSS	Spleen	Spleen

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