Variant report

Variant	rs240308
Chromosome Location	chr6:80659049-80659050
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	YY1	chr6:80658940-80659260	SK-N-SH_RA	brain:	n/a	n/a
2	YY1	chr6:80658956-80659182	K562	blood:	n/a	n/a
3	CTCF	chr6:80658978-80659164	GM19239	blood:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
4	CTCF	chr6:80658980-80659130	HCFaa	heart:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
5	CTCF	chr6:80658920-80659070	HMEC	breast:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
6	CTCF	chr6:80658991-80659150	GM19240	blood:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
7	CTCF	chr6:80659028-80659128	MCF-7	breast:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
8	ZNF143	chr6:80658889-80659228	H1-hESC	embryonic stem cell:	n/a	chr6:80658909-80658928
9	GATA3	chr6:80658694-80659243	MCF-7	breast:	n/a	n/a
10	CTCF	chr6:80658828-80659325	GM12878	blood:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
11	CTCF	chr6:80658668-80659376	A549	lung:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
12	CTCF	chr6:80658923-80659176	MCF-7	breast:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
13	CTCF	chr6:80658960-80659110	GM12867	blood:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
14	RAD21	chr6:80658816-80659293	H1-hESC	embryonic stem cell:	n/a	chr6:80659036-80659055
15	CTCF	chr6:80658960-80659110	HA-sp	spinal cord:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
16	CTCF	chr6:80658940-80659090	HRPEpiC	eye:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
17	CTCF	chr6:80658951-80659134	GM10248	blood:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
18	CTCF	chr6:80659000-80659150	GM12801	blood:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
19	CTCF	chr6:80658940-80659090	AoAF	blood vessel:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
20	CTCF	chr6:80659000-80659150	BJ	skin:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
21	CTCF	chr6:80658865-80659156	SK-N-SH_RA	brain:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
22	RAD21	chr6:80658872-80659271	HepG2	liver:	n/a	chr6:80659036-80659055
23	GATA3	chr6:80658844-80659226	T-47D	breast:	n/a	n/a
24	CTCF	chr6:80658900-80659050	GM12874	blood:	n/a	n/a
25	CTCF	chr6:80658980-80659130	GM12874	blood:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
26	RAD21	chr6:80658759-80659329	ECC-1	luminal epithelium:	n/a	chr6:80659036-80659055
27	RAD21	chr6:80658633-80659500	SK-N-SH	brain:	n/a	chr6:80659036-80659055
28	CTCF	chr6:80658797-80659258	HepG2	liver:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
29	CTCF	chr6:80658937-80659161	MCF-7	breast:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
30	CTCF	chr6:80658866-80659225	K562	blood:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
31	RAD21	chr6:80658831-80659258	GM12878	blood:	n/a	chr6:80659036-80659055
32	CTCF	chr6:80658980-80659130	HCPEpiC	choroid plexus:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
33	RAD21	chr6:80658788-80659349	H1-hESC	embryonic stem cell:	n/a	chr6:80659036-80659055
34	CTCF	chr6:80658914-80659200	H1-hESC	embryonic stem cell:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
35	CTCF	chr6:80658926-80659148	Lung_OC	lung:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
36	CTCF	chr6:80658960-80659110	HVMF	connective:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
37	RAD21	chr6:80658851-80659339	HepG2	liver:	n/a	chr6:80659036-80659055
38	CTCF	chr6:80658960-80659110	AG04449	skin:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
39	CTCF	chr6:80658941-80659156	ProgFib	skin:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
40	TEAD4	chr6:80658835-80659207	K562	blood:	n/a	n/a
41	WRNIP1	chr6:80659004-80659274	GM12878	blood:	n/a	n/a
42	CTCF	chr6:80658721-80659403	HCT-116	colon:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
43	CTCF	chr6:80658960-80659110	HMF	breast:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
44	CTCF	chr6:80658920-80659070	NHDF-neo	bronchial:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
45	CTCF	chr6:80658940-80659090	AG04450	lung:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
46	CTCF	chr6:80658959-80659161	Kidney_OC	kidney:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
47	CTCF	chr6:80658858-80659181	T-47D	breast:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
48	CTCF	chr6:80658975-80659135	GM20000	blood:	n/a	chr6:80659035-80659053 chr6:80659037-80659058
49	SMC3	chr6:80658864-80659359	GM12878	blood:	n/a	n/a
50	CTCF	chr6:80659020-80659170	GM12866	blood:	n/a	chr6:80659035-80659053 chr6:80659037-80659058

No.	Distal block	Cell Line	Cell type
1	chr6:80658870..80659475-chr6:80804226..80804935,2	MCF-7	breast:
2	chr6:80657745..80660049-chr6:80716512..80719051,2	MCF-7	breast:
3	chr6:80658835..80659700-chr6:80713034..80713810,2	MCF-7	breast:
4	chr6:80658511..80659143-chr6:80803528..80804503,2	K562	blood:
5	chr6:80658533..80659818-chr6:80802938..80804495,11	MCF-7	breast:
6	chr6:80658920..80659483-chr6:80801274..80801876,2	K562	blood:

Variant related genes	Relation type
ELOVL4	TF binding region
ENSG00000112742	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs151584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs151673	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs186915	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs239507	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs239509	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239540	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs239542	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs239543	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs239544	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs240323	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs647044	0.92[AMR][1000 genomes];0.96[EUR][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	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv3475140	chr6:80592690-80679283	Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv3475142	chr6:80592789-80679132	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv933704	chr6:80657182-80674202	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80655600-80659400	Active TSS	Thymus	Thymus
2	chr6:80657800-80659200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:80657800-80659800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr6:80658000-80659200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:80658000-80660600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:80658000-80664200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:80658600-80659200	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr6:80658800-80659200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:80658800-80659400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr6:80658800-80659400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:80658800-80659800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:80659000-80659200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr6:80659000-80659200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr6:80659000-80659200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:80659000-80659200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr6:80659000-80659200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:80659000-80659400	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr6:80659000-80659400	Active TSS	Primary T cells from cord blood	blood
19	chr6:80659000-80659400	Enhancers	Primary T cells fromperipheralblood	blood
20	chr6:80659000-80659400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:80659000-80659400	Flanking Active TSS	Liver	Liver
22	chr6:80659000-80659400	Flanking Active TSS	Fetal Thymus	thymus
23	chr6:80659000-80659400	Enhancers	Gastric	stomach
24	chr6:80659000-80659400	Enhancers	Stomach Mucosa	stomach
25	chr6:80659000-80659400	Flanking Active TSS	Dnd41	blood
26	chr6:80659000-80659400	Active TSS	GM12878-XiMat	blood
27	chr6:80659000-80659400	Active TSS	Hela-S3	cervix

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