Variant report

Variant	rs540014430
Chromosome Location	chr6:30883567-30883568
allele	C/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	RAD21	chr6:30883309-30883569	K562	blood:	n/a	chr6:30883454-30883473
2	ZNF384	chr6:30883330-30883643	GM12878	blood:	n/a	n/a
3	RAD21	chr6:30883036-30883836	HCT-116	colon:	n/a	chr6:30883454-30883473
4	CTCF	chr6:30883321-30883600	MCF-7	breast:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
5	CTCF	chr6:30883335-30883601	Hela-S3	cervix:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
6	CTCF	chr6:30881367-30884041	SK-N-SH	brain:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
7	RAD21	chr6:30882997-30883889	HCT-116	colon:	n/a	chr6:30883454-30883473
8	POLR2A	chr6:30883417-30884112	K562	blood:	n/a	n/a
9	CTCF	chr6:30883336-30883612	SK-N-SH_RA	brain:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
10	CTCF	chr6:30883145-30883803	HCT-116	colon:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
11	POLR2A	chr6:30881501-30883780	SK-N-MC	brain:	n/a	n/a
12	RAD21	chr6:30883284-30883644	HepG2	liver:	n/a	chr6:30883454-30883473
13	CTCF	chr6:30883351-30883615	GM19240	blood:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
14	RAD21	chr6:30883210-30883774	HepG2	liver:	n/a	chr6:30883454-30883473
15	ZNF143	chr6:30883290-30883644	GM12878	blood:	n/a	n/a
16	NR2F2	chr6:30883270-30883657	K562	blood:	n/a	n/a
17	SMC3	chr6:30883222-30883692	K562	blood:	n/a	n/a
18	ZNF143	chr6:30882780-30883610	K562	blood:	n/a	chr6:30883075-30883094
19	BHLHE40	chr6:30883403-30883759	K562	blood:	n/a	n/a
20	CTCF	chr6:30883294-30883618	Kidney_OC	kidney:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
21	CTCF	chr6:30883347-30883600	ECC-1	luminal epithelium:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
22	CTCF	chr6:30883331-30883580	Pancreas_OC	pancreas:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
23	CTCF	chr6:30883371-30883578	GM13976	blood:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
24	CTCF	chr6:30883208-30883676	HepG2	liver:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
25	CTCF	chr6:30883279-30883594	T-47D	breast:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
26	RAD21	chr6:30883236-30883637	K562	blood:	n/a	chr6:30883454-30883473
27	CTCF	chr6:30883219-30883674	T-47D	breast:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
28	CTCF	chr6:30883255-30883663	A549	lung:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
29	CTCF	chr6:30883360-30883575	GM10248	blood:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
30	CTCF	chr6:30883315-30883610	A549	lung:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
31	POLR2A	chr6:30881436-30884176	HepG2	liver:	n/a	n/a
32	RAD21	chr6:30883215-30883644	A549	lung:	n/a	chr6:30883454-30883473
33	UBTF	chr6:30883398-30883569	K562	blood:	n/a	n/a
34	JUND	chr6:30883284-30883593	K562	blood:	n/a	n/a
35	RAD21	chr6:30883183-30883754	MCF-7	breast:	n/a	chr6:30883454-30883473
36	RAD21	chr6:30883289-30883643	K562	blood:	n/a	chr6:30883454-30883473
37	CTCF	chr6:30883238-30883684	K562	blood:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
38	CTCF	chr6:30883197-30883667	GM12878	blood:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
39	RAD21	chr6:30883199-30883819	MCF-7	breast:	n/a	chr6:30883454-30883473
40	SMC3	chr6:30883262-30883665	HepG2	liver:	n/a	n/a
41	WRNIP1	chr6:30883347-30883567	GM12878	blood:	n/a	n/a
42	RCOR1	chr6:30883243-30883602	K562	blood:	n/a	n/a
43	RAD21	chr6:30883255-30883688	GM12878	blood:	n/a	chr6:30883454-30883473
44	CTCF	chr6:30883420-30883570	Caco-2	colon:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
45	TEAD4	chr6:30881721-30883771	K562	blood:	n/a	n/a
46	CTCF	chr6:30883294-30883605	GM12878	blood:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
47	RAD21	chr6:30882942-30884015	SK-N-SH	brain:	n/a	chr6:30883454-30883473
48	CTCF	chr6:30883279-30883640	A549	lung:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
49	CTCF	chr6:30883167-30883672	MCF-7	breast:	n/a	chr6:30883455-30883476 chr6:30883454-30883470
50	CTCF	chr6:30883235-30883657	H1-hESC	embryonic stem cell:	n/a	chr6:30883455-30883476 chr6:30883454-30883470

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30883526-30883576	HRE	kidney:	n/a
2	chr6:30883526-30883576	BE2_C	brain:	n/a
3	chr6:30883526-30883576	HCT-116	colon:	n/a
4	chr6:30883526-30883576	GM19239	blood:	n/a
5	chr6:30883526-30883576	HepG2	liver:	n/a
6	chr6:30883526-30883576	HCM	heart:	n/a
7	chr6:30883526-30883576	GM12878	blood:	n/a
8	chr6:30883526-30883576	MCF-7	breast:	n/a
9	chr6:30883526-30883576	GM06990	blood:	n/a
10	chr6:30883526-30883576	HEEpiC	esophagus:	n/a
11	chr6:30883526-30883576	HL-60	blood:	n/a
12	chr6:30883526-30883576	HCF	heart:	n/a
13	chr6:30883526-30883576	BJ	skin:	n/a
14	chr6:30883526-30883576	SK-N-SH	brain:	n/a
15	chr6:30883526-30883576	IMR90	lung:	fetal
16	chr6:30883526-30883576	PrEC	prostate:	n/a
17	chr6:30883526-30883576	U87	brain:	n/a
18	chr6:30883526-30883576	NB4	blood:	n/a
19	chr6:30883526-30883576	CMK	blood:	n/a
20	chr6:30883526-30883576	MCF10A-Er-Src	breast:	n/a
21	chr6:30883526-30883576	HIPEpiC	eye:	n/a
22	chr6:30883526-30883576	HAEpiC	amniotic membrane:	n/a
23	chr6:30883526-30883576	NT2-D1	testis:	n/a
24	chr6:30883526-30883576	Caco-2	colon:	n/a
25	chr6:30883526-30883576	T-47D	breast:	n/a
26	chr6:30883526-30883576	HCPEpiC	choroid plexus:	n/a
27	chr6:30883526-30883576	SK-N-MC	brain:	n/a
28	chr6:30883526-30883576	HUVEC	blood vessel:	n/a
29	chr6:30883526-30883576	ovcar-3	ovarian:	n/a
30	chr6:30883526-30883576	GM12892	blood:	n/a
31	chr6:30883526-30883576	AG09319	gingival:	n/a
32	chr6:30883526-30883576	A549	lung:	n/a
33	chr6:30883526-30883576	NH-A	brain:	n/a
34	chr6:30883526-30883576	HPAEpiC	pulmonary alveolar:	n/a
35	chr6:30883526-30883576	AoSMC	blood vessel:	n/a
36	chr6:30883526-30883576	HRPEpiC	eye:	n/a
37	chr6:30883526-30883576	GM12891	blood:	n/a
38	chr6:30883526-30883576	LNCaP	prostate:	n/a
39	chr6:30883526-30883576	H1-hESC	embryonic stem cell:	embryo
40	chr6:30883526-30883576	AG04450	lung:	fetal
41	chr6:30883526-30883576	HMEC	breast:	n/a
42	chr6:30883526-30883576	SKMC	muscle:	n/a
43	chr6:30883526-30883576	Hela-S3	cervix:	n/a
44	chr6:30883526-30883576	HNPCEpiC	eye:	n/a
45	chr6:30883526-30883576	ECC-1	luminal epithelium:	n/a
46	chr6:30883526-30883576	AG04449	skin:	fetal
47	chr6:30883526-30883576	ProgFib	skin:	n/a
48	chr6:30883526-30883576	SAEC	small airway:	n/a
49	chr6:30883526-30883576	HRCEpiC	kidney:	n/a
50	chr6:30883526-30883576	PFSK-1	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30883403..30884976-chr6:30908264..30911485,3	MCF-7	breast:
2	chr6:30883149..30883983-chr6:31038127..31038765,2	MCF-7	breast:
3	chr6:30883032..30883759-chr6:31011810..31012818,4	MCF-7	breast:
4	chr6:30850549..30855941-chr6:30880357..30883667,13	MCF-7	breast:
5	chr6:30793814..30798702-chr6:30880453..30884092,5	K562	blood:
6	chr6:30847750..30854588-chr6:30880214..30885422,8	K562	blood:
7	chr6:30882036..30883658-chr6:31081525..31084682,3	MCF-7	breast:
8	chr6:30523025..30525668-chr6:30880813..30884106,3	K562	blood:
9	chr6:30882935..30883738-chr6:31047207..31048204,5	MCF-7	breast:
10	chr6:30882943..30883998-chr6:31010336..31011408,3	MCF-7	breast:
11	chr6:30882042..30885135-chr6:30886350..30889389,4	MCF-7	breast:
12	chr6:30844121..30846194-chr6:30880539..30883879,3	K562	blood:
13	chr6:30883250..30883934-chr6:31010475..31011616,5	MCF-7	breast:
14	chr6:30882873..30883896-chr6:31038173..31038772,3	K562	blood:
15	chr6:30881968..30885056-chr6:30885339..30888267,3	MCF-7	breast:
16	chr6:30882829..30883945-chr6:31036385..31037390,5	MCF-7	breast:
17	chr6:30789462..30790321-chr6:30882992..30883906,2	K562	blood:
18	chr6:30854396..30859063-chr6:30880954..30884819,5	K562	blood:

Variant related genes	Relation type
VARS2	TF binding region
VARS2	CpG island
ENSG00000214894	Chromatin interaction
ENSG00000264594	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000168631	Chromatin interaction
ENSG00000204540	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000204576	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	chr6:30882200-30883600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:30882200-30883800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:30882200-30883800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr6:30882200-30883800	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr6:30882200-30884000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr6:30882400-30883600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:30882400-30883600	Flanking Active TSS	Brain Hippocampus Middle	brain
10	chr6:30882400-30883600	Flanking Active TSS	Dnd41	blood
11	chr6:30882400-30883600	Flanking Active TSS	NHEK	skin
12	chr6:30882600-30883800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:30882600-30884000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:30882600-30884000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:30882600-30884000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:30882600-30884800	Weak transcription	Aorta	Aorta
17	chr6:30882600-30885000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:30882600-30885000	Enhancers	Lung	lung
19	chr6:30882600-30886800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:30882800-30883600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr6:30882800-30883600	Enhancers	Primary B cells from peripheral blood	blood
22	chr6:30882800-30883600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr6:30882800-30883600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:30882800-30883600	Enhancers	Brain Cingulate Gyrus	brain
25	chr6:30882800-30883600	Enhancers	Fetal Muscle Leg	muscle
26	chr6:30882800-30883600	Flanking Active TSS	HepG2	liver
27	chr6:30882800-30883800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr6:30882800-30883800	Enhancers	Primary T cells fromperipheralblood	blood
29	chr6:30882800-30883800	Enhancers	Gastric	stomach
30	chr6:30882800-30883800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr6:30882800-30883800	Enhancers	Psoas Muscle	Psoas
32	chr6:30882800-30883800	Enhancers	Right Atrium	heart
33	chr6:30882800-30883800	Enhancers	Right Ventricle	heart
34	chr6:30882800-30883800	Enhancers	A549	lung
35	chr6:30882800-30883800	Enhancers	Osteobl	bone
36	chr6:30882800-30884000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:30882800-30884000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:30882800-30884000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:30882800-30884000	Enhancers	Left Ventricle	heart
40	chr6:30882800-30884000	Enhancers	Spleen	Spleen
41	chr6:30882800-30884200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:30882800-30884200	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr6:30882800-30884200	Enhancers	Fetal Brain Male	brain
44	chr6:30882800-30884600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr6:30882800-30884600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:30882800-30884600	Weak transcription	Ovary	ovary
47	chr6:30882800-30884800	Enhancers	HUVEC	blood vessel
48	chr6:30882800-30890200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr6:30882800-30890200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:30883000-30883600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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