Variant report

Variant	rs947358
Chromosome Location	chr6:128841945-128841946
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	CTCF	chr6:128841820-128841970	GM12866	blood:	n/a	chr6:128841849-128841867 chr6:128841851-128841864
2	POLR2A	chr6:128841413-128842128	HCT-116	colon:	n/a	n/a
3	CTCF	chr6:128841691-128842017	MCF-7	breast:	n/a	chr6:128841849-128841867 chr6:128841851-128841864
4	TBP	chr6:128840196-128842291	H1-hESC	embryonic stem cell:	n/a	n/a
5	TEAD4	chr6:128841319-128842741	SK-N-SH	brain:	n/a	n/a
6	NANOG	chr6:128841589-128842016	H1-hESC	embryonic stem cell:	n/a	n/a
7	TCF7L2	chr6:128841175-128842386	HCT-116	colon:	n/a	n/a
8	REST	chr6:128841372-128842071	SK-N-SH	brain:	n/a	chr6:128841707-128841720 chr6:128841921-128841934 chr6:128841577-128841590
9	POLR2A	chr6:128841464-128842121	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:128840188-128842148	GM18526	blood:	n/a	n/a
11	HEY1	chr6:128841364-128842221	HepG2	liver:	n/a	chr6:128841690-128841705 chr6:128841692-128841707 chr6:128841828-128841843
12	RFX5	chr6:128841058-128842059	HepG2	liver:	n/a	n/a
13	MAZ	chr6:128841559-128842388	HepG2	liver:	n/a	n/a
14	BRCA1	chr6:128841550-128842404	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr6:128841311-128842081	MCF-7	breast:	n/a	chr6:128841849-128841867 chr6:128841851-128841864
16	TAF1	chr6:128840069-128842287	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr6:128840676-128842221	ECC-1	luminal epithelium:	n/a	n/a
18	CTCF	chr6:128841695-128841984	NHEK	skin:	n/a	chr6:128841849-128841867 chr6:128841851-128841864
19	CEBPD	chr6:128841510-128842107	HepG2	liver:	n/a	n/a
20	YY1	chr6:128840718-128842154	SK-N-SH	brain:	n/a	chr6:128841835-128841849 chr6:128841920-128841934 chr6:128841922-128841931 chr6:128841697-128841706 chr6:128841847-128841861 chr6:128841840-128841849 chr6:128841697-128841711 chr6:128841694-128841708
21	POLR2A	chr6:128841298-128842210	ECC-1	luminal epithelium:	n/a	n/a
22	CTCF	chr6:128841691-128842026	MCF-7	breast:	n/a	chr6:128841849-128841867 chr6:128841851-128841864
23	TAF7	chr6:128841369-128842079	H1-hESC	embryonic stem cell:	n/a	n/a
24	GTF2F1	chr6:128841535-128842070	Hela-S3	cervix:	n/a	n/a
25	MYC	chr6:128841680-128842159	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr6:128840623-128842208	ECC-1	luminal epithelium:	n/a	chr6:128841389-128841399
27	CTCF	chr6:128841737-128841992	Spleen_OC	spleen:	n/a	chr6:128841849-128841867 chr6:128841851-128841864
28	RAD21	chr6:128841460-128842800	Hela-S3	cervix:	n/a	chr6:128841979-128841991 chr6:128841929-128841943
29	POLR2A	chr6:128841465-128842194	HUVEC	blood vessel:	n/a	n/a
30	FOXA1	chr6:128841718-128841950	T-47D	breast:	n/a	n/a
31	PAX5	chr6:128841759-128841971	GM12892	blood:	n/a	n/a
32	POLR2A	chr6:128841338-128842324	HUVEC	blood vessel:	n/a	n/a
33	HNF4A	chr6:128841475-128842115	HepG2	liver:	n/a	n/a
34	KAP1	chr6:128841870-128842671	U2OS	brain:	n/a	chr6:128842058-128842066
35	SIN3AK20	chr6:128841578-128842167	H1-hESC	embryonic stem cell:	n/a	n/a
36	CREB1	chr6:128841379-128842058	H1-hESC	embryonic stem cell:	n/a	chr6:128841786-128841799 chr6:128841786-128841799
37	POLR2A	chr6:128841507-128842051	A549	lung:	n/a	n/a
38	CTCF	chr6:128841703-128842038	GM19238	blood:	n/a	chr6:128841849-128841867 chr6:128841851-128841864
39	CTCF	chr6:128841766-128841947	LNCaP	prostate:	n/a	chr6:128841849-128841867 chr6:128841851-128841864
40	FOSL1	chr6:128841784-128842126	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr6:128841338-128842117	HepG2	liver:	n/a	n/a
42	RAD21	chr6:128841679-128842215	A549	lung:	n/a	chr6:128841979-128841991 chr6:128841929-128841943
43	ZKSCAN1	chr6:128841128-128842252	Hela-S3	cervix:	n/a	n/a
44	TAF1	chr6:128841009-128842299	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr6:128840014-128842191	H1-hESC	embryonic stem cell:	n/a	n/a
46	RAD21	chr6:128841646-128842051	HepG2	liver:	n/a	chr6:128841979-128841991 chr6:128841929-128841943
47	POLR2A	chr6:128840184-128842177	MCF-7	breast:	n/a	n/a
48	TCF12	chr6:128839932-128842908	SK-N-SH	brain:	n/a	chr6:128842311-128842318
49	YY1	chr6:128840083-128842019	H1-hESC	embryonic stem cell:	n/a	chr6:128841835-128841849 chr6:128841920-128841934 chr6:128841922-128841931 chr6:128841697-128841706 chr6:128841847-128841861 chr6:128841840-128841849 chr6:128841697-128841711 chr6:128841694-128841708
50	RFX5	chr6:128841455-128841990	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:128529927..128532522-chr6:128841893..128843396,2	MCF-7	breast:
2	chr16:75143191..75144858-chr6:128840309..128843134,2	MCF-7	breast:
3	chr6:128819294..128822394-chr6:128840492..128843286,6	MCF-7	breast:
4	chr6:128817983..128822479-chr6:128839649..128843314,6	MCF-7	breast:
5	chr6:128810906..128814817-chr6:128838628..128842024,3	MCF-7	breast:

Variant related genes	Relation type
PTPRK	TF binding region
ENSG00000247033	Chromatin interaction
ENSG00000152894	Chromatin interaction
ENSG00000224733	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10085247	0.87[EUR][1000 genomes]
rs10085248	0.87[EUR][1000 genomes]
rs10223535	0.83[EUR][1000 genomes]
rs10872331	0.83[EUR][1000 genomes]
rs11154439	0.83[EUR][1000 genomes]
rs11963575	0.84[EUR][1000 genomes]
rs13209380	0.82[AMR][1000 genomes]
rs1361595	0.83[EUR][1000 genomes]
rs17055938	1.00[ASN][1000 genomes]
rs17055952	0.87[EUR][1000 genomes]
rs60719752	1.00[ASN][1000 genomes]
rs62426794	0.88[EUR][1000 genomes]
rs6569533	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6916193	0.82[AMR][1000 genomes]
rs6920943	0.82[AMR][1000 genomes]
rs6923822	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6924111	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6935611	0.82[AMR][1000 genomes]
rs7356912	0.87[EUR][1000 genomes]
rs73772047	0.87[ASN][1000 genomes]
rs7745291	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9321121	0.87[ASN][1000 genomes]
rs9375570	0.87[ASN][1000 genomes]
rs9375575	0.81[EUR][1000 genomes]
rs9388638	0.87[ASN][1000 genomes]
rs9482893	0.83[EUR][1000 genomes]
rs9491990	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9491997	0.82[AMR][1000 genomes]
rs9491999	0.85[AMR][1000 genomes]
rs9492001	0.82[AMR][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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer 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
4	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128837200-128842800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr6:128838200-128842400	Active TSS	Brain Cingulate Gyrus	brain
3	chr6:128838400-128842200	Active TSS	Duodenum Mucosa	Duodenum
4	chr6:128838400-128843000	Active TSS	Fetal Brain Male	brain
5	chr6:128838600-128842200	Active TSS	HMEC	breast
6	chr6:128838600-128842400	Active TSS	Fetal Intestine Small	intestine
7	chr6:128838600-128842600	Active TSS	Brain Hippocampus Middle	brain
8	chr6:128838600-128842600	Active TSS	Fetal Intestine Large	intestine
9	chr6:128838600-128842800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:128838600-128842800	Active TSS	Brain Angular Gyrus	brain
11	chr6:128838800-128842400	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr6:128838800-128842600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:128838800-128842800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:128838800-128842800	Active TSS	Stomach Smooth Muscle	stomach
15	chr6:128839000-128842400	Active TSS	NH-A	brain
16	chr6:128839200-128842800	Active TSS	Right Atrium	heart
17	chr6:128839400-128842000	Active TSS	Fetal Thymus	thymus
18	chr6:128839400-128842200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:128839400-128842600	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr6:128839400-128842600	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr6:128839400-128842600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:128839400-128842600	Active TSS	Brain Anterior Caudate	brain
23	chr6:128839400-128842600	Active TSS	Colonic Mucosa	Colon
24	chr6:128839400-128842600	Active TSS	Fetal Heart	heart
25	chr6:128839400-128842600	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr6:128839400-128842600	Active TSS	NHDF-Ad	bronchial
27	chr6:128839400-128842800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:128839400-128842800	Active TSS	HSMMtube	muscle
29	chr6:128839600-128842200	Active TSS	Gastric	stomach
30	chr6:128839600-128842400	Active TSS	Colon Smooth Muscle	Colon
31	chr6:128839600-128842400	Active TSS	Ovary	ovary
32	chr6:128839600-128842400	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr6:128839600-128842400	Bivalent/Poised TSS	HepG2	liver
34	chr6:128839600-128842400	Active TSS	NHEK	skin
35	chr6:128839600-128842600	Active TSS	Left Ventricle	heart
36	chr6:128839600-128842600	Active TSS	Pancreas	Pancrea
37	chr6:128839600-128842600	Active TSS	Rectal Smooth Muscle	rectum
38	chr6:128839600-128842600	Active TSS	A549	lung
39	chr6:128839600-128842600	Active TSS	NHLF	lung
40	chr6:128839800-128842400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr6:128839800-128842400	Active TSS	Aorta	Aorta
42	chr6:128839800-128842400	Active TSS	Lung	lung
43	chr6:128839800-128842400	Active TSS	Small Intestine	intestine
44	chr6:128839800-128842600	Active TSS	H9 Cell Line	embryonic stem cell
45	chr6:128839800-128842600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:128839800-128842600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr6:128839800-128842600	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr6:128839800-128842600	Active TSS	Psoas Muscle	Psoas
49	chr6:128840000-128842200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:128840000-128842200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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