Variant report

Variant	rs542730
Chromosome Location	chr13:30687118-30687119
allele	G/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	CHD1	chr13:30686603-30687550	IMR90	lung:	n/a	n/a
2	MXI1	chr13:30686565-30687978	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr13:30687069-30687444	SK-N-SH_RA	brain:	n/a	n/a
4	SMC3	chr13:30687009-30687561	GM12878	blood:	n/a	n/a
5	CTCF	chr13:30687112-30687417	Kidney_OC	kidney:	n/a	chr13:30687266-30687282
6	YY1	chr13:30687015-30687457	SK-N-SH_RA	brain:	n/a	n/a
7	RAD21	chr13:30687077-30687449	A549	lung:	n/a	n/a
8	YY1	chr13:30687038-30687404	HepG2	liver:	n/a	n/a
9	ZNF143	chr13:30687097-30687445	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr13:30687084-30687368	K562	blood:	n/a	chr13:30687266-30687282
11	USF2	chr13:30686934-30687265	Hela-S3	cervix:	n/a	n/a
12	YY1	chr13:30687018-30687486	SK-N-SH	brain:	n/a	n/a
13	CTCF	chr13:30687090-30687458	Spleen_OC	spleen:	n/a	chr13:30687266-30687282
14	MAX	chr13:30686798-30687576	NB4	blood:	n/a	chr13:30686970-30686981 chr13:30686967-30686982 chr13:30686971-30686981 chr13:30686969-30686982 chr13:30686971-30686980 chr13:30686969-30686982 chr13:30686970-30686981
15	RCOR1	chr13:30687093-30687379	K562	blood:	n/a	n/a
16	MAFK	chr13:30687107-30687465	IMR90	lung:	n/a	chr13:30687220-30687236
17	CTCF	chr13:30687093-30687429	T-47D	breast:	n/a	chr13:30687266-30687282
18	TBL1XR1	chr13:30686955-30687434	GM12878	blood:	n/a	n/a
19	CTCF	chr13:30686983-30687582	HCT-116	colon:	n/a	chr13:30687266-30687282
20	CHD1	chr13:30687118-30687439	GM12878	blood:	n/a	n/a
21	TEAD4	chr13:30686931-30687468	H1-hESC	embryonic stem cell:	n/a	n/a
22	SMC3	chr13:30686989-30687469	Hela-S3	cervix:	n/a	n/a
23	YY1	chr13:30687039-30687390	GM12892	blood:	n/a	n/a
24	MAFK	chr13:30687005-30687422	Hela-S3	cervix:	n/a	chr13:30687220-30687236
25	CTCF	chr13:30686860-30687642	A549	lung:	n/a	chr13:30687266-30687282
26	JUND	chr13:30687099-30687427	H1-hESC	embryonic stem cell:	n/a	n/a
27	RAD21	chr13:30685907-30687893	SK-N-SH	brain:	n/a	chr13:30686289-30686301
28	CTCF	chr13:30687043-30687494	GM12878	blood:	n/a	chr13:30687266-30687282
29	YY1	chr13:30686895-30687470	H1-hESC	embryonic stem cell:	n/a	n/a
30	RCOR1	chr13:30687080-30687439	GM12878	blood:	n/a	n/a
31	CTCF	chr13:30687042-30687404	HepG2	liver:	n/a	chr13:30687266-30687282
32	GTF2F1	chr13:30687105-30687441	Hela-S3	cervix:	n/a	n/a
33	ARID3A	chr13:30687027-30687469	HepG2	liver:	n/a	n/a
34	CTCF	chr13:30687112-30687399	H1-hESC	embryonic stem cell:	n/a	chr13:30687266-30687282
35	CTCF	chr13:30687052-30687495	IMR90	lung:	n/a	chr13:30687266-30687282
36	BCLAF1	chr13:30687050-30687527	GM12878	blood:	n/a	n/a
37	YY1	chr13:30687090-30687360	K562	blood:	n/a	n/a
38	ZNF143	chr13:30687086-30687474	GM12878	blood:	n/a	n/a
39	CTCF	chr13:30687054-30687444	ECC-1	luminal epithelium:	n/a	chr13:30687266-30687282
40	RAD21	chr13:30687108-30687366	K562	blood:	n/a	n/a
41	YY1	chr13:30687057-30687495	SK-N-SH_RA	brain:	n/a	n/a
42	ATF2	chr13:30687012-30687374	H1-hESC	embryonic stem cell:	n/a	n/a
43	RAD21	chr13:30686995-30687546	MCF-7	breast:	n/a	n/a
44	TAF1	chr13:30687023-30687436	ECC-1	luminal epithelium:	n/a	n/a
45	MXI1	chr13:30686944-30687357	Hela-S3	cervix:	n/a	n/a
46	YY1	chr13:30687046-30687368	HepG2	liver:	n/a	n/a
47	RAD21	chr13:30686978-30687417	HepG2	liver:	n/a	n/a
48	SIN3A	chr13:30686880-30687400	H1-hESC	embryonic stem cell:	n/a	n/a
49	YY1	chr13:30687045-30687435	GM12891	blood:	n/a	n/a
50	SMC3	chr13:30687044-30687481	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:30421278..30427133-chr13:30682148..30691157,22	MCF-7	breast:
2	chr13:30511863..30512590-chr13:30686869..30687418,2	MCF-7	breast:
3	chr13:30344222..30347052-chr13:30686907..30688799,2	MCF-7	breast:
4	chr13:30422658..30425963-chr13:30681369..30690318,16	MCF-7	breast:
5	chr13:30419487..30420690-chr13:30686853..30688126,3	MCF-7	breast:
6	chr13:30403000..30404793-chr13:30686519..30690620,3	MCF-7	breast:
7	chr13:30494996..30500904-chr13:30681667..30688775,12	MCF-7	breast:
8	chr13:30681522..30684361-chr13:30684383..30687280,3	MCF-7	breast:
9	chr13:30419310..30420181-chr13:30687018..30687782,2	K562	blood:
10	chr13:30680284..30681903-chr13:30686575..30689356,2	K562	blood:
11	chr13:30498368..30498950-chr13:30686816..30687387,2	MCF-7	breast:
12	chr13:30268179..30269731-chr13:30686906..30689381,2	MCF-7	breast:
13	chr13:30687032..30689624-chr13:30701987..30704608,2	MCF-7	breast:
14	chr13:30342827..30348055-chr13:30683488..30688791,7	MCF-7	breast:
15	chr13:30415961..30419397-chr13:30686617..30690558,4	MCF-7	breast:
16	chr13:30676534..30678418-chr13:30686349..30688302,2	MCF-7	breast:
17	chr13:30495539..30501420-chr13:30683250..30690010,13	MCF-7	breast:
18	chr13:30686343..30690173-chr13:31036596..31040141,3	MCF-7	breast:

Variant related genes	Relation type
LINC00365	TF binding region
ENSG00000224405	Chromatin interaction
ENSG00000224511	Chromatin interaction
ENSG00000189403	Chromatin interaction
ENSG00000122043	Chromatin interaction
ENSG00000122042	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs57613215	1.00[EUR][1000 genomes]
rs61064633	1.00[EUR][1000 genomes]
rs73454490	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040215	chr13:30621351-30741022	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541745	chr13:30621351-30741022	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv832572	chr13:30650005-30835256	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30679000-30687800	Weak transcription	Small Intestine	intestine
2	chr13:30679800-30687600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr13:30680200-30688000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr13:30681200-30687200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:30682000-30688400	Weak transcription	Spleen	Spleen
6	chr13:30682800-30688600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr13:30683400-30688800	Weak transcription	Lung	lung
8	chr13:30683600-30687800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:30683600-30687800	Weak transcription	Colonic Mucosa	Colon
10	chr13:30683600-30688000	Weak transcription	Pancreas	Pancrea
11	chr13:30683600-30688800	Weak transcription	Esophagus	oesophagus
12	chr13:30683800-30688600	Weak transcription	Right Atrium	heart
13	chr13:30684400-30687600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr13:30684800-30688400	Weak transcription	Right Ventricle	heart
15	chr13:30685000-30687400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr13:30685200-30688200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr13:30685800-30688000	Enhancers	Stomach Mucosa	stomach
18	chr13:30686000-30688200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr13:30686000-30688200	Enhancers	Fetal Intestine Small	intestine
20	chr13:30686200-30687200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr13:30686200-30687600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
22	chr13:30686200-30687800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
23	chr13:30686400-30687600	Enhancers	Fetal Lung	lung
24	chr13:30686600-30687200	Enhancers	Primary hematopoietic stem cells	blood
25	chr13:30686600-30687200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr13:30686600-30687200	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr13:30686600-30687200	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr13:30686600-30687200	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr13:30686600-30687200	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr13:30686600-30687200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr13:30686600-30687200	Enhancers	Fetal Heart	heart
32	chr13:30686600-30687400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr13:30686600-30687400	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr13:30686600-30687600	Enhancers	Fetal Brain Male	brain
35	chr13:30686600-30688400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr13:30686600-30688400	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr13:30686600-30688400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr13:30686600-30688400	Enhancers	Fetal Intestine Large	intestine
39	chr13:30686600-30688600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr13:30686800-30687200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr13:30686800-30687200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr13:30686800-30687200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr13:30686800-30687200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr13:30686800-30687200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr13:30686800-30687200	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr13:30686800-30687200	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr13:30686800-30687200	Enhancers	Primary B cells from cord blood	blood
48	chr13:30686800-30687200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr13:30686800-30687200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr13:30686800-30687200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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