Variant report

Variant	rs539036441
Chromosome Location	chr6:30883307-30883308
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	CHD2	chr6:30881944-30883329	K562	blood:	n/a	n/a
2	RAD21	chr6:30883036-30883836	HCT-116	colon:	n/a	chr6:30883454-30883473
3	CTCF	chr6:30881367-30884041	SK-N-SH	brain:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
4	RAD21	chr6:30882997-30883889	HCT-116	colon:	n/a	chr6:30883454-30883473
5	CTCF	chr6:30883145-30883803	HCT-116	colon:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
6	POLR2A	chr6:30881501-30883780	SK-N-MC	brain:	n/a	n/a
7	RAD21	chr6:30883284-30883644	HepG2	liver:	n/a	chr6:30883454-30883473
8	POLR2A	chr6:30881632-30883343	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr6:30883210-30883774	HepG2	liver:	n/a	chr6:30883454-30883473
10	ZNF143	chr6:30883290-30883644	GM12878	blood:	n/a	n/a
11	NR2F2	chr6:30883270-30883657	K562	blood:	n/a	n/a
12	SMC3	chr6:30883222-30883692	K562	blood:	n/a	n/a
13	ZNF143	chr6:30882780-30883610	K562	blood:	n/a	chr6:30883075-30883094
14	CTCF	chr6:30883294-30883618	Kidney_OC	kidney:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
15	CTCF	chr6:30883208-30883676	HepG2	liver:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
16	CTCF	chr6:30883279-30883594	T-47D	breast:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
17	RAD21	chr6:30883236-30883637	K562	blood:	n/a	chr6:30883454-30883473
18	CTCF	chr6:30883219-30883674	T-47D	breast:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
19	CTCF	chr6:30883255-30883663	A549	lung:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
20	POLR2A	chr6:30881436-30884176	HepG2	liver:	n/a	n/a
21	RAD21	chr6:30883215-30883644	A549	lung:	n/a	chr6:30883454-30883473
22	JUND	chr6:30883284-30883593	K562	blood:	n/a	n/a
23	RAD21	chr6:30883183-30883754	MCF-7	breast:	n/a	chr6:30883454-30883473
24	PML	chr6:30881732-30883476	K562	blood:	n/a	chr6:30882918-30882926
25	RAD21	chr6:30883289-30883643	K562	blood:	n/a	chr6:30883454-30883473
26	CTCF	chr6:30883238-30883684	K562	blood:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
27	CTCF	chr6:30883197-30883667	GM12878	blood:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
28	MAZ	chr6:30883224-30883361	HepG2	liver:	n/a	n/a
29	RAD21	chr6:30883199-30883819	MCF-7	breast:	n/a	chr6:30883454-30883473
30	SMC3	chr6:30883262-30883665	HepG2	liver:	n/a	n/a
31	POLR2A	chr6:30883226-30883406	H1-hESC	embryonic stem cell:	n/a	n/a
32	RCOR1	chr6:30883243-30883602	K562	blood:	n/a	n/a
33	RAD21	chr6:30883255-30883688	GM12878	blood:	n/a	chr6:30883454-30883473
34	TEAD4	chr6:30881721-30883771	K562	blood:	n/a	n/a
35	POLR2A	chr6:30881853-30883329	K562	blood:	n/a	n/a
36	CTCF	chr6:30883294-30883605	GM12878	blood:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
37	CTCF	chr6:30883280-30883430	WI-38	lung:	n/a	n/a
38	RAD21	chr6:30882942-30884015	SK-N-SH	brain:	n/a	chr6:30883454-30883473
39	CTCF	chr6:30883279-30883640	A549	lung:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
40	CTCF	chr6:30883167-30883672	MCF-7	breast:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
41	CTCF	chr6:30883235-30883657	H1-hESC	embryonic stem cell:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
42	CTCF	chr6:30883149-30883721	MCF-7	breast:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
43	RAD21	chr6:30883162-30883755	IMR90	lung:	n/a	chr6:30883454-30883473
44	CTCF	chr6:30882881-30883783	A549	lung:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
45	POLR2A	chr6:30881359-30883343	K562	blood:	n/a	n/a
46	RAD21	chr6:30883214-30883710	ECC-1	luminal epithelium:	n/a	chr6:30883454-30883473
47	POLR2A	chr6:30883266-30883397	ProgFib	skin:	n/a	n/a
48	MYBL2	chr6:30882854-30883641	HepG2	liver:	n/a	n/a
49	CTCF	chr6:30883300-30883450	HFF-Myc	foreskin:	n/a	n/a
50	CTCF	chr6:30883275-30883724	K562	blood:	n/a	chr6:30883455-30883476 chr6:30883454-30883470

No.	Distal block	Cell Line	Cell type
1	chr6:30883149..30883983-chr6:31038127..31038765,2	MCF-7	breast:
2	chr6:30883032..30883759-chr6:31011810..31012818,4	MCF-7	breast:
3	chr6:30850549..30855941-chr6:30880357..30883667,13	MCF-7	breast:
4	chr6:30793814..30798702-chr6:30880453..30884092,5	K562	blood:
5	chr6:30847750..30854588-chr6:30880214..30885422,8	K562	blood:
6	chr6:30880736..30883349-chr6:30890122..30892611,2	MCF-7	breast:
7	chr6:30882036..30883658-chr6:31081525..31084682,3	MCF-7	breast:
8	chr6:30881341..30883528-chr6:31050692..31052360,2	K562	blood:
9	chr6:30523025..30525668-chr6:30880813..30884106,3	K562	blood:
10	chr6:30882935..30883738-chr6:31047207..31048204,5	MCF-7	breast:
11	chr6:30882943..30883998-chr6:31010336..31011408,3	MCF-7	breast:
12	chr6:30881805..30883309-chr6:31050438..31053270,2	MCF-7	breast:
13	chr6:30882042..30885135-chr6:30886350..30889389,4	MCF-7	breast:
14	chr6:30844121..30846194-chr6:30880539..30883879,3	K562	blood:
15	chr6:30883250..30883934-chr6:31010475..31011616,5	MCF-7	breast:
16	chr6:30882873..30883896-chr6:31038173..31038772,3	K562	blood:
17	chr6:30882744..30883495-chr6:31055361..31056022,2	K562	blood:
18	chr6:30881968..30885056-chr6:30885339..30888267,3	MCF-7	breast:
19	chr6:30882829..30883945-chr6:31036385..31037390,5	MCF-7	breast:
20	chr6:30789462..30790321-chr6:30882992..30883906,2	K562	blood:
21	chr6:30854396..30859063-chr6:30880954..30884819,5	K562	blood:
22	chr6:30881341..30883550-chr6:31049543..31052360,3	K562	blood:
23	chr6:30707880..30713865-chr6:30880456..30883497,7	MCF-7	breast:
24	chr6:30709387..30712006-chr6:30881214..30883426,2	K562	blood:

Variant related genes	Relation type
VARS2	TF binding region
ENSG00000137411	Chromatin interaction
ENSG00000222895	Chromatin interaction
ENSG00000214894	Chromatin interaction
ENSG00000204540	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000264594	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000137331	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1031677	chr6:30857542-30972865	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv525438	chr6:30864829-30933975	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv523346	chr6:30882513-30893941	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30881400-30883600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:30881400-30884200	Active TSS	Esophagus	oesophagus
3	chr6:30882200-30883400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr6:30882200-30883400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:30882200-30883400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:30882200-30883400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:30882200-30883400	Flanking Active TSS	Liver	Liver
8	chr6:30882200-30883400	Flanking Active TSS	Fetal Lung	lung
9	chr6:30882200-30883400	Flanking Active TSS	Hela-S3	cervix
10	chr6:30882200-30883600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:30882200-30883800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:30882200-30883800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr6:30882200-30883800	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr6:30882200-30884000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr6:30882400-30883400	Flanking Active TSS	Colon Smooth Muscle	Colon
16	chr6:30882400-30883400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr6:30882400-30883400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr6:30882400-30883400	Transcr. at gene 5' and 3'	K562	blood
19	chr6:30882400-30883600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:30882400-30883600	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr6:30882400-30883600	Flanking Active TSS	Dnd41	blood
22	chr6:30882400-30883600	Flanking Active TSS	NHEK	skin
23	chr6:30882600-30883400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr6:30882600-30883400	Flanking Active TSS	Rectal Smooth Muscle	rectum
25	chr6:30882600-30883400	Flanking Active TSS	GM12878-XiMat	blood
26	chr6:30882600-30883800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:30882600-30884000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:30882600-30884000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:30882600-30884000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:30882600-30884800	Weak transcription	Aorta	Aorta
31	chr6:30882600-30885000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:30882600-30885000	Enhancers	Lung	lung
33	chr6:30882600-30886800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:30882800-30883400	Enhancers	Primary B cells from cord blood	blood
35	chr6:30882800-30883400	Enhancers	Primary T cells from cord blood	blood
36	chr6:30882800-30883400	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr6:30882800-30883400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:30882800-30883400	Enhancers	Stomach Mucosa	stomach
39	chr6:30882800-30883400	Enhancers	HSMMtube	muscle
40	chr6:30882800-30883600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr6:30882800-30883600	Enhancers	Primary B cells from peripheral blood	blood
42	chr6:30882800-30883600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr6:30882800-30883600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:30882800-30883600	Enhancers	Brain Cingulate Gyrus	brain
45	chr6:30882800-30883600	Enhancers	Fetal Muscle Leg	muscle
46	chr6:30882800-30883600	Flanking Active TSS	HepG2	liver
47	chr6:30882800-30883800	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr6:30882800-30883800	Enhancers	Primary T cells fromperipheralblood	blood
49	chr6:30882800-30883800	Enhancers	Gastric	stomach
50	chr6:30882800-30883800	Enhancers	Placenta Amnion	Placenta Amnion

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