Variant report

Variant	rs62400773
Chromosome Location	chr6:24646197-24646198
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	USF2	chr6:24645673-24646375	Hela-S3	cervix:	n/a	chr6:24646128-24646144
2	POLR2A	chr6:24645852-24646654	H1-neurons	neurons:	n/a	n/a
3	TFAP2C	chr6:24645783-24647140	Hela-S3	cervix:	n/a	n/a
4	EP300	chr6:24645948-24646530	GM12878	blood:	n/a	chr6:24646286-24646302 chr6:24646361-24646377 chr6:24646283-24646292
5	POLR2A	chr6:24646124-24646751	Gliobla	brain:	n/a	n/a
6	BHLHE40	chr6:24646144-24646408	K562	blood:	n/a	chr6:24646366-24646382
7	BRCA1	chr6:24645385-24646255	Hela-S3	cervix:	n/a	n/a
8	NR2F2	chr6:24646046-24646680	MCF-7	breast:	n/a	n/a
9	HA-E2F1	chr6:24645763-24646810	MCF-7	breast:	n/a	chr6:24646299-24646309 chr6:24646421-24646428 chr6:24646458-24646467 chr6:24646283-24646293
10	RCOR1	chr6:24645789-24646496	GM12878	blood:	n/a	n/a
11	MYC	chr6:24645849-24646567	K562	blood:	n/a	n/a
12	POLR2A	chr6:24645813-24646740	Hela-S3	cervix:	n/a	n/a
13	MXI1	chr6:24645895-24647439	IMR90	lung:	n/a	chr6:24646440-24646455 chr6:24646438-24646453
14	MAX	chr6:24646019-24646717	A549	lung:	n/a	n/a
15	RAD21	chr6:24645737-24646725	H1-hESC	embryonic stem cell:	n/a	chr6:24646315-24646328 chr6:24646379-24646393
16	HA-E2F1	chr6:24645889-24646665	Hela-S3	cervix:	n/a	chr6:24646299-24646309 chr6:24646421-24646428 chr6:24646458-24646467 chr6:24646283-24646293
17	MXI1	chr6:24646086-24646619	HepG2	liver:	n/a	chr6:24646440-24646455 chr6:24646438-24646453
18	TFAP2A	chr6:24645759-24647092	Hela-S3	cervix:	n/a	n/a
19	MAX	chr6:24645854-24646582	ECC-1	luminal epithelium:	n/a	n/a
20	MAX	chr6:24645832-24646533	ECC-1	luminal epithelium:	n/a	n/a
21	FOXA2	chr6:24645903-24646490	A549	lung:	n/a	n/a
22	POLR2A	chr6:24646153-24646468	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr6:24645848-24646691	Raji	blood:	n/a	n/a
24	HCFC1	chr6:24646156-24646700	K562	blood:	n/a	n/a
25	POLR2A	chr6:24645971-24646683	A549	lung:	n/a	n/a
26	KAP1	chr6:24645725-24646364	HEK293	kidney:	n/a	n/a
27	SIN3A	chr6:24646112-24646485	GM12878	blood:	n/a	chr6:24646289-24646302
28	MAX	chr6:24645767-24646663	H1-hESC	embryonic stem cell:	n/a	n/a
29	RFX5	chr6:24645329-24647270	Hela-S3	cervix:	n/a	chr6:24646439-24646454 chr6:24646439-24646454 chr6:24646438-24646455 chr6:24646439-24646454
30	POLR2A	chr6:24646070-24646723	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr6:24645929-24646738	MCF-7	breast:	n/a	n/a
32	MAX	chr6:24645834-24646605	A549	lung:	n/a	n/a
33	E2F1	chr6:24645930-24646636	Hela-S3	cervix:	n/a	chr6:24646299-24646309 chr6:24646421-24646428 chr6:24646458-24646467 chr6:24646283-24646293
34	SIN3AK20	chr6:24646132-24646466	HepG2	liver:	n/a	n/a
35	ZKSCAN1	chr6:24645612-24646582	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr6:24645874-24646677	A549	lung:	n/a	n/a
37	MAX	chr6:24646132-24646503	K562	blood:	n/a	n/a
38	EP300	chr6:24646153-24646518	HepG2	liver:	n/a	chr6:24646286-24646302 chr6:24646361-24646377 chr6:24646283-24646292
39	CHD2	chr6:24645960-24646680	GM12878	blood:	n/a	chr6:24646421-24646428
40	JUND	chr6:24646133-24646597	A549	lung:	n/a	n/a
41	RAD21	chr6:24646141-24646673	HepG2	liver:	n/a	chr6:24646315-24646328 chr6:24646379-24646393
42	MYC	chr6:24645839-24646591	K562	blood:	n/a	n/a
43	ZNF143	chr6:24646018-24646479	GM12878	blood:	n/a	chr6:24646367-24646377
44	CTCF	chr6:24646113-24646352	MCF-7	breast:	n/a	chr6:24646137-24646145
45	FOS	chr6:24646196-24646606	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr6:24645885-24646608	A549	lung:	n/a	n/a
47	BHLHE40	chr6:24645994-24646433	GM12878	blood:	n/a	chr6:24646366-24646382 chr6:24646128-24646144
48	POLR2A	chr6:24645688-24646651	Hela-S3	cervix:	n/a	n/a
49	SMARCC1	chr6:24645792-24646882	Hela-S3	cervix:	n/a	n/a
50	RCOR1	chr6:24645755-24646929	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:24644992..24647314-chr6:24719656..24721157,2	MCF-7	breast:
2	chr6:24645396..24648521-chr6:24658092..24661192,3	K562	blood:
3	chr6:24645218..24647641-chr6:24665331..24668427,5	MCF-7	breast:
4	chr6:24645863..24648986-chr6:24665821..24668897,5	MCF-7	breast:
5	chr6:24645396..24648552-chr6:24658188..24661192,4	K562	blood:
6	chr6:24645670..24648708-chr6:24654981..24659486,5	MCF-7	breast:
7	chr1:162530645..162531244-chr6:24645762..24646411,2	Hela-S3	cervix:

Variant related genes	Relation type
KIAA0319	TF binding region
ENSG00000259788	Chromatin interaction
ENSG00000112308	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000111802	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11559067	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889567	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17243136	0.82[EUR][1000 genomes]
rs17243276	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249561	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249729	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17412874	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17419844	1.00[ASN][1000 genomes]
rs17491730	1.00[ASN][1000 genomes]
rs3212238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400556	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400558	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400559	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400760	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400783	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400786	1.00[ASN][1000 genomes]
rs62400787	1.00[ASN][1000 genomes]
rs62400789	1.00[ASN][1000 genomes]
rs62400790	1.00[ASN][1000 genomes]
rs62400792	1.00[ASN][1000 genomes]
rs62400793	1.00[ASN][1000 genomes]
rs62400795	1.00[ASN][1000 genomes]
rs62400819	1.00[ASN][1000 genomes]
rs62402860	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62402863	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62402864	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv601164	chr6:24625091-24661599	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv601165	chr6:24632642-24666007	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 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	chr6:24643600-24647000	Active TSS	Fetal Brain Female	brain
2	chr6:24644000-24646800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr6:24644000-24647000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr6:24644200-24647000	Active TSS	Brain Anterior Caudate	brain
5	chr6:24645400-24647000	Active TSS	Brain Angular Gyrus	brain
6	chr6:24645600-24646200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:24645600-24646200	Flanking Bivalent TSS/Enh	Dnd41	blood
8	chr6:24645600-24646400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:24645600-24646600	Active TSS	Colon Smooth Muscle	Colon
10	chr6:24645600-24646600	Active TSS	A549	lung
11	chr6:24645600-24646600	Active TSS	Hela-S3	cervix
12	chr6:24645600-24646800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:24645600-24646800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr6:24645600-24646800	Active TSS	Brain Germinal Matrix	brain
15	chr6:24645600-24646800	Active TSS	Brain Substantia Nigra	brain
16	chr6:24645600-24647000	Active TSS	H1 Cell Line	embryonic stem cell
17	chr6:24645600-24647000	Active TSS	H9 Cell Line	embryonic stem cell
18	chr6:24645600-24647000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr6:24645600-24647000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:24645600-24647000	Active TSS	Brain Cingulate Gyrus	brain
21	chr6:24645600-24647000	Active TSS	Brain Hippocampus Middle	brain
22	chr6:24645600-24647000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:24645600-24647000	Flanking Active TSS	GM12878-XiMat	blood
24	chr6:24645600-24647000	Flanking Active TSS	NHEK	skin
25	chr6:24645800-24646200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:24645800-24646200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:24645800-24646200	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:24645800-24646200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr6:24645800-24646200	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr6:24645800-24646200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
31	chr6:24645800-24646200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr6:24645800-24646200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:24645800-24646200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:24645800-24646200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:24645800-24646200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr6:24645800-24646200	Active TSS	Colonic Mucosa	Colon
37	chr6:24645800-24646200	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr6:24645800-24646200	Flanking Active TSS	Esophagus	oesophagus
39	chr6:24645800-24646200	Flanking Active TSS	Fetal Brain Male	brain
40	chr6:24645800-24646200	Flanking Bivalent TSS/Enh	Fetal Lung	lung
41	chr6:24645800-24646200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
42	chr6:24645800-24646200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
43	chr6:24645800-24646200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
44	chr6:24645800-24646200	Flanking Active TSS	Left Ventricle	heart
45	chr6:24645800-24646200	Enhancers	Lung	lung
46	chr6:24645800-24646200	Enhancers	Placenta Amnion	Placenta Amnion
47	chr6:24645800-24646200	Flanking Active TSS	Right Ventricle	heart
48	chr6:24645800-24646200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr6:24645800-24646200	Flanking Bivalent TSS/Enh	HSMM	muscle
50	chr6:24645800-24646200	Flanking Active TSS	K562	blood

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