Variant report

Variant	rs72860099
Chromosome Location	chr6:28911585-28911586
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	JUND	chr6:28911330-28911673	A549	lung:	n/a	n/a
2	BACH1	chr6:28911341-28911672	H1-hESC	embryonic stem cell:	n/a	n/a
3	SP1	chr6:28911226-28911683	GM12878	blood:	n/a	chr6:28911570-28911584 chr6:28911527-28911534
4	MTA3	chr6:28911534-28912539	GM12878	blood:	n/a	n/a
5	MTA3	chr6:28911178-28912616	GM12878	blood:	n/a	n/a
6	BDP1	chr6:28911327-28911719	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr6:28911291-28911679	HepG2	liver:	n/a	n/a
8	YY1	chr6:28911255-28911738	HepG2	liver:	n/a	n/a
9	GTF2F1	chr6:28911165-28911677	K562	blood:	n/a	n/a
10	GTF3C2	chr6:28910983-28911776	K562	blood:	n/a	n/a
11	IRF1	chr6:28911183-28911697	K562	blood:	n/a	chr6:28911500-28911514 chr6:28911501-28911515 chr6:28911495-28911516 chr6:28911499-28911510 chr6:28911500-28911513 chr6:28911500-28911513 chr6:28911497-28911511 chr6:28911500-28911511 chr6:28911501-28911511
12	RAD21	chr6:28911360-28911668	SK-N-SH_RA	brain:	n/a	n/a
13	ZKSCAN1	chr6:28911500-28911695	Hela-S3	cervix:	n/a	n/a
14	GTF2F1	chr6:28911311-28912515	Hela-S3	cervix:	n/a	n/a
15	ATF3	chr6:28911012-28911867	A549	lung:	n/a	n/a
16	ELF1	chr6:28911306-28911909	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:28911027-28911627	K562	blood:	n/a	n/a
18	MBD4	chr6:28911084-28911967	HepG2	liver:	n/a	n/a
19	SIN3A	chr6:28911180-28912489	H1-hESC	embryonic stem cell:	n/a	n/a
20	TEAD4	chr6:28911233-28911795	H1-hESC	embryonic stem cell:	n/a	n/a
21	TEAD4	chr6:28911251-28911756	A549	lung:	n/a	n/a
22	MYBL2	chr6:28911035-28911828	HepG2	liver:	n/a	n/a
23	NR2F2	chr6:28910796-28912776	K562	blood:	n/a	n/a
24	SIN3AK20	chr6:28911294-28911599	A549	lung:	n/a	n/a
25	POLR2A	chr6:28911170-28911638	PANC-1	pancreas:	n/a	n/a
26	TEAD4	chr6:28910944-28912774	HepG2	liver:	n/a	n/a
27	EGR1	chr6:28911374-28911614	GM12878	blood:	n/a	n/a
28	GABPA	chr6:28911230-28911614	Hela-S3	cervix:	n/a	n/a
29	YY1	chr6:28911208-28911585	K562	blood:	n/a	n/a
30	HMGN3	chr6:28911186-28911597	K562	blood:	n/a	n/a
31	YY1	chr6:28911329-28911601	A549	lung:	n/a	n/a
32	CTCF	chr6:28911480-28911630	AG10803	skin:	n/a	n/a
33	IRF1	chr6:28911292-28911633	K562	blood:	n/a	chr6:28911500-28911514 chr6:28911501-28911515 chr6:28911495-28911516 chr6:28911499-28911510 chr6:28911500-28911513 chr6:28911500-28911513 chr6:28911497-28911511 chr6:28911500-28911511 chr6:28911501-28911511
34	EP300	chr6:28910905-28911835	K562	blood:	n/a	chr6:28911283-28911297
35	HSF1	chr6:28911202-28911661	HepG2	liver:	n/a	n/a
36	TAF1	chr6:28911470-28911911	K562	blood:	n/a	n/a
37	CTCF	chr6:28911520-28911670	GM12867	blood:	n/a	n/a
38	MAX	chr6:28911299-28911659	NB4	blood:	n/a	n/a
39	BHLHE40	chr6:28911293-28911723	K562	blood:	n/a	n/a
40	ATF3	chr6:28910961-28912792	A549	lung:	n/a	n/a
41	ELF1	chr6:28911317-28911903	HepG2	liver:	n/a	n/a
42	NRF1	chr6:28911324-28911656	H1-hESC	embryonic stem cell:	n/a	n/a
43	UBTF	chr6:28911196-28911683	K562	blood:	n/a	n/a
44	SP1	chr6:28911142-28911695	A549	lung:	n/a	chr6:28911570-28911584 chr6:28911527-28911534
45	TEAD4	chr6:28910938-28912912	K562	blood:	n/a	n/a
46	ZNF143	chr6:28911185-28911678	K562	blood:	n/a	n/a
47	ARID3A	chr6:28911238-28911775	HepG2	liver:	n/a	n/a
48	MAFF	chr6:28911343-28911813	HepG2	liver:	n/a	n/a
49	RAD21	chr6:28911375-28911790	HepG2	liver:	n/a	n/a
50	CEBPB	chr6:28911338-28911675	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:28888957..28894217-chr6:28902105..28913114,27	MCF-7	breast:
2	chr6:28859278..28869415-chr6:28906395..28912460,18	K562	blood:
3	chr6:28583985..28585633-chr6:28910730..28913227,2	K562	blood:
4	chr6:28886838..28893375-chr6:28904762..28912890,19	K562	blood:
5	chr6:28803772..28808857-chr6:28906937..28913057,11	K562	blood:
6	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
7	chr6:27775703..27777987-chr6:28908653..28911644,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf100-11	chr6:28911561-28912315	NONHSAT108497

Variant related genes	Relation type
C6orf100	TF binding region
ENSG00000225173	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000232040	Chromatin interaction
ENSG00000263426	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000203813	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1041881	0.81[EUR][1000 genomes]
rs1056032	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12194037	0.97[EUR][1000 genomes]
rs17399888	0.86[EUR][1000 genomes]
rs2071786	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2071787	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2071788	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28531681	0.83[EUR][1000 genomes]
rs2894065	0.87[EUR][1000 genomes]
rs3763338	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3763339	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4713180	0.81[EUR][1000 genomes]
rs4713182	0.87[EUR][1000 genomes]
rs4713183	0.91[EUR][1000 genomes]
rs4713184	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4713191	0.91[EUR][1000 genomes]
rs4713195	0.85[EUR][1000 genomes]
rs4713196	0.85[EUR][1000 genomes]
rs4947256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61751894	0.88[EUR][1000 genomes]
rs6928948	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6936343	0.85[EUR][1000 genomes]
rs72853516	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72853522	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72853523	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72860085	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72862420	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72862423	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73741203	0.87[EUR][1000 genomes]
rs743848	0.84[EUR][1000 genomes]
rs7745220	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7761745	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7762289	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9295782	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9366731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366733	0.83[EUR][1000 genomes]
rs9380098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9380100	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380102	0.90[EUR][1000 genomes]
rs9380103	0.83[EUR][1000 genomes]
rs968723	0.91[EUR][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	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28906600-28912600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:28907400-28912400	Active TSS	H1 Cell Line	embryonic stem cell
3	chr6:28907400-28912400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:28907400-28912400	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr6:28907400-28912400	Active TSS	A549	lung
6	chr6:28907400-28912800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:28907400-28913400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:28907800-28912400	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr6:28907800-28912400	Active TSS	Rectal Smooth Muscle	rectum
10	chr6:28909800-28911600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:28910200-28912400	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr6:28910200-28912400	Active TSS	Brain Angular Gyrus	brain
13	chr6:28910600-28912400	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr6:28910800-28911600	Active TSS	HepG2	liver
15	chr6:28911000-28911600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:28911000-28911600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:28911000-28911600	Enhancers	Esophagus	oesophagus
18	chr6:28911000-28911600	Active TSS	Fetal Lung	lung
19	chr6:28911000-28911800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr6:28911000-28912000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr6:28911000-28912000	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr6:28911000-28912000	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr6:28911000-28912200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:28911000-28912200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr6:28911000-28912200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr6:28911000-28912400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:28911000-28912400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:28911000-28912400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:28911000-28912400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:28911000-28912400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:28911000-28912400	Active TSS	Brain Substantia Nigra	brain
32	chr6:28911000-28912400	Active TSS	Colon Smooth Muscle	Colon
33	chr6:28911000-28912400	Active TSS	Right Ventricle	heart
34	chr6:28911000-28912600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:28911000-28912600	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr6:28911000-28912600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:28911000-28912600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr6:28911000-28912600	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr6:28911000-28912600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:28911000-28912800	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr6:28911200-28911600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:28911200-28911600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:28911200-28911600	Active TSS	Duodenum Mucosa	Duodenum
44	chr6:28911200-28911600	Bivalent/Poised TSS	Fetal Brain Male	brain
45	chr6:28911200-28911600	Active TSS	Fetal Intestine Small	intestine
46	chr6:28911200-28911600	Active TSS	Left Ventricle	heart
47	chr6:28911200-28911600	Active TSS	Psoas Muscle	Psoas
48	chr6:28911200-28911600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
49	chr6:28911200-28911600	Enhancers	Spleen	Spleen
50	chr6:28911200-28911600	Active TSS	GM12878-XiMat	blood

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