Variant report

Variant	rs4712841
Chromosome Location	chr6:24722309-24722310
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	EBF1	chr6:24720953-24722332	GM12878	blood:	n/a	n/a
2	RCOR1	chr6:24720378-24722426	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:24719540-24722490	NB4	blood:	n/a	n/a
4	BHLHE40	chr6:24720460-24722377	K562	blood:	n/a	chr6:24720625-24720641 chr6:24720633-24720649 chr6:24721097-24721113
5	POLR2A	chr6:24717288-24722666	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr6:24720241-24722389	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr6:24719329-24722375	ProgFib	skin:	n/a	n/a
8	JUN	chr6:24720841-24722394	K562	blood:	n/a	chr6:24721563-24721574 chr6:24720993-24721002 chr6:24720994-24721003
9	POLR2A	chr6:24719230-24722689	GM19193	blood:	n/a	n/a
10	POLR2A	chr6:24719246-24722397	GM19099	blood:	n/a	n/a
11	ZNF143	chr6:24720801-24722325	K562	blood:	n/a	n/a
12	POLR2A	chr6:24721466-24722426	GM12891	blood:	n/a	n/a
13	MAX	chr6:24720243-24722330	HepG2	liver:	n/a	chr6:24721856-24721863 chr6:24720992-24721002 chr6:24721851-24721866 chr6:24721855-24721864 chr6:24721855-24721864
14	TEAD4	chr6:24720850-24722427	HepG2	liver:	n/a	n/a
15	POLR2A	chr6:24718493-24722658	H1-hESC	embryonic stem cell:	n/a	n/a
16	NFATC1	chr6:24721484-24722543	GM12878	blood:	n/a	n/a
17	MXI1	chr6:24717374-24722519	SK-N-SH	brain:	n/a	n/a
18	HEY1	chr6:24721358-24722455	HepG2	liver:	n/a	n/a
19	CHD1	chr6:24721748-24722421	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr6:24720218-24722664	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr6:24717443-24722588	IMR90	lung:	n/a	n/a
22	HCFC1	chr6:24719293-24722417	Hela-S3	cervix:	n/a	n/a
23	TEAD4	chr6:24720506-24722439	K562	blood:	n/a	n/a
24	TBP	chr6:24720689-24722426	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:24718370-24722530	GM12892	blood:	n/a	n/a
26	SP1	chr6:24720536-24722335	HCT-116	colon:	n/a	chr6:24720791-24720805 chr6:24721422-24721433 chr6:24721389-24721399 chr6:24721472-24721481 chr6:24721471-24721483 chr6:24721652-24721661 chr6:24721647-24721661 chr6:24721473-24721482 chr6:24721471-24721483 chr6:24721472-24721481
27	POLR2A	chr6:24718706-24722605	GM12892	blood:	n/a	n/a
28	NFIC	chr6:24720788-24722427	HepG2	liver:	n/a	n/a
29	MBD4	chr6:24720546-24722493	HepG2	liver:	n/a	n/a
30	GTF2F1	chr6:24720860-24722360	K562	blood:	n/a	n/a
31	MBD4	chr6:24720512-24722470	HepG2	liver:	n/a	n/a
32	POLR2A	chr6:24719382-24722558	GM12878	blood:	n/a	n/a
33	SMC3	chr6:24720893-24722313	HepG2	liver:	n/a	n/a
34	EP300	chr6:24720866-24722325	GM12878	blood:	n/a	chr6:24721864-24721880 chr6:24721242-24721256 chr6:24721663-24721677 chr6:24721338-24721351
35	E2F6	chr6:24721368-24722359	A549	lung:	n/a	n/a
36	FOXA1	chr6:24721876-24722429	HepG2	liver:	n/a	n/a
37	JUND	chr6:24720424-24722376	SK-N-SH	brain:	n/a	chr6:24721563-24721574 chr6:24720993-24721002 chr6:24720994-24721003
38	POLR2A	chr6:24720259-24722442	PFSK-1	brain:	n/a	n/a
39	TAL1	chr6:24719214-24722485	K562	blood:	n/a	n/a
40	POLR2A	chr6:24718365-24722644	GM12878	blood:	n/a	n/a
41	POLR2A	chr6:24718256-24722451	HepG2	liver:	n/a	n/a
42	MAZ	chr6:24719353-24722341	IMR90	lung:	n/a	chr6:24719353-24719363 chr6:24721856-24721863 chr6:24720992-24721002 chr6:24721851-24721866 chr6:24721855-24721864 chr6:24721855-24721864
43	HEY1	chr6:24721399-24722540	HepG2	liver:	n/a	n/a
44	MYC	chr6:24719543-24722380	K562	blood:	n/a	chr6:24721856-24721863 chr6:24720992-24721002 chr6:24721851-24721866 chr6:24721855-24721864 chr6:24721855-24721864
45	HEY1	chr6:24721347-24722488	K562	blood:	n/a	n/a
46	MAX	chr6:24720811-24722360	MCF-7	breast:	n/a	chr6:24721856-24721863 chr6:24720992-24721002 chr6:24721851-24721866 chr6:24721855-24721864 chr6:24721855-24721864
47	MYBL2	chr6:24720515-24722415	HepG2	liver:	n/a	n/a
48	POLR2A	chr6:24717757-24722547	GM12878	blood:	n/a	n/a
49	EP300	chr6:24720831-24722344	K562	blood:	n/a	chr6:24721864-24721880 chr6:24721242-24721256 chr6:24721663-24721677 chr6:24721338-24721351
50	POLR2A	chr6:24721373-24722516	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:24711892..24724164-chr6:24769415..24786834,81	K562	blood:
2	chr6:24721486..24723774-chr6:24748539..24750202,2	K562	blood:
3	chr6:24719506..24722494-chr6:24741132..24743826,4	K562	blood:
4	chr6:24721787..24724500-chr6:24751636..24753786,2	MCF-7	breast:
5	chr6:24657655..24659922-chr6:24720349..24722391,2	K562	blood:
6	chr6:24715365..24725462-chr6:24770390..24783002,86	K562	blood:
7	chr6:24718870..24722603-chr6:26025035..26028594,6	K562	blood:
8	chr6:24696748..24707740-chr6:24716503..24724189,24	MCF-7	breast:
9	chr5:36241334..36243447-chr6:24720553..24722359,2	K562	blood:
10	chr6:24493014..24496474-chr6:24718971..24722650,4	K562	blood:
11	chr6:24718549..24722818-chr6:24771512..24777723,8	MCF-7	breast:
12	chr6:24661385..24670379-chr6:24713871..24722680,32	K562	blood:
13	chr6:24659286..24660892-chr6:24721746..24723397,2	MCF-7	breast:
14	chr6:24717870..24723661-chr6:24773711..24778808,16	MCF-7	breast:
15	chr6:24660920..24672880-chr6:24713381..24723000,42	K562	blood:
16	chr6:24720760..24722445-chr6:24809512..24811592,2	K562	blood:
17	chr14:53416668..53418435-chr6:24720286..24722655,2	MCF-7	breast:
18	chr6:20401095..20405762-chr6:24718847..24722714,7	K562	blood:
19	chr6:20400126..20404982-chr6:24718144..24722714,11	K562	blood:
20	chr6:24719452..24722494-chr6:24742032..24745228,7	K562	blood:

Variant related genes	Relation type
C6orf62	TF binding region
ENSG00000272345	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000073712	Chromatin interaction
ENSG00000272402	Chromatin interaction
ENSG00000112294	Chromatin interaction
ENSG00000112242	Chromatin interaction
ENSG00000111802	Chromatin interaction
ENSG00000111913	Chromatin interaction
ENSG00000224164	Chromatin interaction
ENSG00000218806	Chromatin interaction
ENSG00000112312	Chromatin interaction
ENSG00000152620	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000112293	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10806992	0.80[ASN][1000 genomes]
rs2038541	0.82[ASN][1000 genomes]
rs2064977	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2145753	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2876673	0.82[ASN][1000 genomes]
rs4712843	0.93[ASN][1000 genomes]
rs6941870	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7762810	0.81[ASN][1000 genomes]
rs9356945	0.81[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	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
4	nsv428474	chr6:24714157-24797977	Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24716400-24722400	Active TSS	Ovary	ovary
2	chr6:24716600-24722400	Active TSS	Right Ventricle	heart
3	chr6:24716800-24722400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:24716800-24722600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr6:24717000-24722400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:24717000-24722400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:24717000-24722400	Active TSS	Brain Angular Gyrus	brain
8	chr6:24717000-24722600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr6:24717800-24722400	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:24717800-24722400	Active TSS	Psoas Muscle	Psoas
11	chr6:24717800-24722400	Active TSS	Thymus	Thymus
12	chr6:24718000-24722400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr6:24718000-24722400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:24718000-24722600	Active TSS	Stomach Smooth Muscle	stomach
15	chr6:24718200-24722400	Active TSS	Brain Anterior Caudate	brain
16	chr6:24718400-24722400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr6:24718800-24722600	Active TSS	NHDF-Ad	bronchial
18	chr6:24719000-24722400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:24719200-24722400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:24719200-24722400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:24719400-24722400	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr6:24719400-24722400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:24719400-24722400	Active TSS	Brain Hippocampus Middle	brain
24	chr6:24719600-24722400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:24719600-24722600	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr6:24719800-24722400	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr6:24719800-24722400	Active TSS	Fetal Brain Male	brain
28	chr6:24719800-24722600	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr6:24719800-24722600	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr6:24719800-24722600	Active TSS	Fetal Brain Female	brain
31	chr6:24720800-24722600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:24721000-24722400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:24721000-24722400	Active TSS	Brain Germinal Matrix	brain
34	chr6:24721000-24722600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:24721200-24722400	Active TSS	Aorta	Aorta
36	chr6:24721200-24722400	Active TSS	Right Atrium	heart
37	chr6:24721800-24722400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr6:24721800-24722400	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr6:24721800-24722400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr6:24721800-24722400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:24721800-24722400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:24721800-24722400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr6:24721800-24722400	Flanking Active TSS	Hela-S3	cervix
44	chr6:24721800-24722400	Flanking Active TSS	HUVEC	blood vessel
45	chr6:24721800-24722400	Flanking Active TSS	NH-A	brain
46	chr6:24721800-24722600	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr6:24721800-24722600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr6:24721800-24722600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr6:24721800-24722600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:24721800-24722600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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