Variant report

Variant	rs59638108
Chromosome Location	chr6:5004457-5004458
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	POLR2A	chr6:5003836-5004585	U87	brain:	n/a	n/a
2	ELK1	chr6:5004129-5004472	GM12878	blood:	n/a	n/a
3	TAF1	chr6:5003600-5004569	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr6:5004207-5004523	Spleen_OC	spleen:	n/a	chr6:5004341-5004350
5	POLR2A	chr6:5003644-5004827	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:5003688-5004557	HCT-116	colon:	n/a	n/a
7	TCF12	chr6:5003666-5004629	A549	lung:	n/a	n/a
8	MXI1	chr6:5003627-5004538	Hela-S3	cervix:	n/a	chr6:5003751-5003760
9	CTCF	chr6:5004254-5004497	Kidney_OC	kidney:	n/a	chr6:5004341-5004350
10	TAF1	chr6:5003999-5004612	K562	blood:	n/a	n/a
11	POLR2A	chr6:5003830-5004591	U87	brain:	n/a	n/a
12	CTCF	chr6:5004320-5004470	AG10803	skin:	n/a	chr6:5004341-5004350
13	MAZ	chr6:5003707-5004821	HepG2	liver:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
14	EP300	chr6:5003642-5004866	HepG2	liver:	n/a	chr6:5003891-5003907 chr6:5004327-5004343 chr6:5003813-5003826
15	RAD21	chr6:5003809-5004560	H1-hESC	embryonic stem cell:	n/a	n/a
16	IRF1	chr6:5003726-5004893	K562	blood:	n/a	chr6:5004545-5004559
17	CTCF	chr6:5004254-5004466	GM13976	blood:	n/a	chr6:5004341-5004350
18	CTCF	chr6:5004001-5004702	K562	blood:	n/a	chr6:5004341-5004350
19	CTCF	chr6:5004111-5004543	K562	blood:	n/a	chr6:5004341-5004350
20	POLR2A	chr6:5004018-5004579	GM12878	blood:	n/a	n/a
21	EP300	chr6:5003760-5004789	GM12878	blood:	n/a	chr6:5003891-5003907 chr6:5004327-5004343 chr6:5003813-5003826
22	MAX	chr6:5003525-5004607	ECC-1	luminal epithelium:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
23	MYC	chr6:5003609-5004827	K562	blood:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
24	UBTF	chr6:5004339-5005084	K562	blood:	n/a	n/a
25	CUX1	chr6:5003914-5005064	K562	blood:	n/a	n/a
26	CTCF	chr6:5004340-5004490	GM12870	blood:	n/a	chr6:5004341-5004350
27	PAX5	chr6:5003745-5004466	GM12878	blood:	n/a	n/a
28	YY1	chr6:5003855-5004606	SK-N-SH	brain:	n/a	n/a
29	TEAD4	chr6:5003761-5004546	K562	blood:	n/a	n/a
30	POLR2A	chr6:5003616-5004747	GM18951	blood:	n/a	n/a
31	CTCF	chr6:5003503-5005179	A549	lung:	n/a	chr6:5004341-5004350
32	CTCF	chr6:5004320-5004470	NHEK	skin:	n/a	chr6:5004341-5004350
33	CTBP2	chr6:5003730-5004643	H1-hESC	embryonic stem cell:	n/a	n/a
34	TEAD4	chr6:5003707-5004566	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr6:5003628-5004534	Hela-S3	cervix:	n/a	n/a
36	ETS1	chr6:5003667-5004559	GM12878	blood:	n/a	chr6:5003970-5003977 chr6:5003914-5003927 chr6:5003915-5003928 chr6:5003916-5003923 chr6:5003966-5003979 chr6:5004344-5004355 chr6:5003965-5003978
37	HCFC1	chr6:5003522-5005044	Hela-S3	cervix:	n/a	n/a
38	CTCF	chr6:5004320-5004470	HUVEC	blood vessel:	n/a	chr6:5004341-5004350
39	MAX	chr6:5003592-5004610	SK-N-SH	brain:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
40	MAX	chr6:5003546-5004563	H1-hESC	embryonic stem cell:	n/a	chr6:5003750-5003760 chr6:5003751-5003758 chr6:5003749-5003760 chr6:5003894-5003903 chr6:5003750-5003759
41	POLR2A	chr6:5003637-5004559	A549	lung:	n/a	n/a
42	RELA	chr6:5003654-5004947	GM15510	blood:	n/a	n/a
43	RELA	chr6:5003697-5005152	GM18505	blood:	n/a	n/a
44	POLR2A	chr6:5003576-5004546	Hela-S3	cervix:	n/a	n/a
45	HEY1	chr6:5003604-5004640	K562	blood:	n/a	chr6:5004338-5004353
46	EP300	chr6:5004226-5004810	HepG2	liver:	n/a	chr6:5004327-5004343
47	POLR2A	chr6:5003622-5004760	K562	blood:	n/a	n/a
48	SIN3AK20	chr6:5003692-5004462	PFSK-1	brain:	n/a	n/a
49	CTCF	chr6:5004191-5004502	GM12891	blood:	n/a	chr6:5004341-5004350
50	BHLHE40	chr6:5003751-5004507	GM12878	blood:	n/a	chr6:5004328-5004344

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:5004418-5004468	A549	lung:	n/a
2	chr6:5004418-5004468	IMR90	lung:	fetal
3	chr6:5004418-5004468	HRCEpiC	kidney:	n/a
4	chr6:5004418-5004468	HNPCEpiC	eye:	n/a
5	chr6:5004418-5004468	PrEC	prostate:	n/a
6	chr6:5004418-5004468	AoSMC	blood vessel:	n/a
7	chr6:5004418-5004468	GM12878	blood:	n/a
8	chr6:5004418-5004468	MCF-7	breast:	n/a
9	chr6:5004412-5004462	PrEC	prostate:	n/a
10	chr6:5004418-5004468	HMEC	breast:	n/a
11	chr6:5004412-5004462	SK-N-MC	brain:	n/a
12	chr6:5004412-5004462	Caco-2	colon:	n/a
13	chr6:5004412-5004462	HCT-116	colon:	n/a
14	chr6:5004412-5004462	HCPEpiC	choroid plexus:	n/a
15	chr6:5004418-5004468	HRPEpiC	eye:	n/a
16	chr6:5004418-5004468	CMK	blood:	n/a
17	chr6:5004418-5004468	HAEpiC	amniotic membrane:	n/a
18	chr6:5004412-5004462	NH-A	brain:	n/a
19	chr6:5004412-5004462	BJ	skin:	n/a
20	chr6:5004418-5004468	NHBE	bronchial:	n/a
21	chr6:5004412-5004462	SK-N-SH_RA	brain:	n/a
22	chr6:5004412-5004462	U87	brain:	n/a
23	chr6:5004418-5004468	AG04450	lung:	fetal
24	chr6:5004412-5004462	GM19239	blood:	n/a
25	chr6:5004412-5004462	NB4	blood:	n/a
26	chr6:5004412-5004462	AoSMC	blood vessel:	n/a
27	chr6:5004418-5004468	HCM	heart:	n/a
28	chr6:5004412-5004462	GM12891	blood:	n/a
29	chr6:5004418-5004468	NT2-D1	testis:	n/a
30	chr6:5004418-5004468	MCF10A-Er-Src	breast:	n/a
31	chr6:5004412-5004462	AG04450	lung:	fetal
32	chr6:5004412-5004462	GM12878	blood:	n/a
33	chr6:5004412-5004462	Hepatocyte	liver:	n/a
34	chr6:5004412-5004462	NHDF-neo	bronchial:	n/a
35	chr6:5004418-5004468	SAEC	small airway:	n/a
36	chr6:5004412-5004462	H1-hESC	embryonic stem cell:	embryo
37	chr6:5004412-5004462	GM06990	blood:	n/a
38	chr6:5004412-5004462	HepG2	liver:	n/a
39	chr6:5004412-5004462	HMEC	breast:	n/a
40	chr6:5004412-5004462	A549	lung:	n/a
41	chr6:5004418-5004468	SKMC	muscle:	n/a
42	chr6:5004418-5004468	H1-hESC	embryonic stem cell:	embryo
43	chr6:5004418-5004468	SK-N-MC	brain:	n/a
44	chr6:5004412-5004462	GM12892	blood:	n/a
45	chr6:5004418-5004468	HIPEpiC	eye:	n/a
46	chr6:5004418-5004468	GM19239	blood:	n/a
47	chr6:5004412-5004462	NT2-D1	testis:	n/a
48	chr6:5004418-5004468	GM06990	blood:	n/a
49	chr6:5004418-5004468	Hepatocyte	liver:	n/a
50	chr6:5004412-5004462	Jurkat	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:5004317..5004944-chr6:5030555..5031426,2	MCF-7	breast:
2	chr6:5004268..5006268-chr6:5028632..5030855,2	K562	blood:
3	chr6:5004308..5006000-chr6:5030652..5032441,2	K562	blood:
4	chr6:4776139..4778956-chr6:5002447..5004557,2	K562	blood:
5	chr6:5002773..5004480-chr6:5029318..5032794,4	MCF-7	breast:

Variant related genes	Relation type
RPP40	TF binding region
RPP40	CpG island
ENSG00000272142	Chromatin interaction
ENSG00000153046	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11970716	0.83[ASN][1000 genomes]
rs12194104	0.80[ASN][1000 genomes]
rs12200195	0.87[ASN][1000 genomes]
rs2793239	0.80[ASN][1000 genomes]
rs57793325	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57919800	0.80[ASN][1000 genomes]
rs59552394	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62385113	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62385115	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62385117	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62385118	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62385119	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62385121	1.00[ASN][1000 genomes]
rs62385122	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62385123	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62385142	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62385148	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62385159	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62386470	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62386471	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73365175	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs811259	0.88[ASN][1000 genomes]
rs9328283	1.00[ASN][1000 genomes]
rs9328284	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 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	chr6:5003000-5004600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr6:5003000-5004800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:5003000-5005000	Active TSS	Brain Anterior Caudate	brain
4	chr6:5003200-5004600	Active TSS	Brain Hippocampus Middle	brain
5	chr6:5003200-5004600	Active TSS	Duodenum Mucosa	Duodenum
6	chr6:5003200-5004600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
7	chr6:5003200-5004600	Active TSS	Hela-S3	cervix
8	chr6:5003200-5004600	Active TSS	Osteobl	bone
9	chr6:5003200-5004800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:5003200-5004800	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr6:5003200-5004800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:5003200-5004800	Active TSS	NHDF-Ad	bronchial
13	chr6:5003200-5004800	Active TSS	NHEK	skin
14	chr6:5003200-5005000	Active TSS	A549	lung
15	chr6:5003200-5005200	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr6:5003200-5005200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:5003400-5004600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:5003400-5004600	Active TSS	Fetal Brain Female	brain
19	chr6:5003400-5004600	Active TSS	Fetal Intestine Large	intestine
20	chr6:5003400-5004600	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr6:5003400-5004600	Active TSS	GM12878-XiMat	blood
22	chr6:5003400-5004600	Active TSS	NH-A	brain
23	chr6:5003400-5004800	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr6:5003400-5004800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:5003400-5004800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:5003400-5004800	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr6:5003400-5004800	Active TSS	HSMM	muscle
28	chr6:5003400-5005200	Active TSS	Psoas Muscle	Psoas
29	chr6:5003600-5004600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:5003600-5004600	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr6:5003600-5004600	Active TSS	Primary T cells from cord blood	blood
32	chr6:5003600-5004600	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr6:5003600-5004600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:5003600-5004600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr6:5003600-5004600	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr6:5003600-5004600	Active TSS	Brain Angular Gyrus	brain
37	chr6:5003600-5004600	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr6:5003600-5004600	Active TSS	Brain Substantia Nigra	brain
39	chr6:5003600-5004600	Active TSS	Pancreas	Pancrea
40	chr6:5003600-5004600	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr6:5003600-5004600	Active TSS	Small Intestine	intestine
42	chr6:5003600-5004600	Active TSS	Stomach Mucosa	stomach
43	chr6:5003600-5004600	Active TSS	Stomach Smooth Muscle	stomach
44	chr6:5003600-5004600	Active TSS	HSMMtube	muscle
45	chr6:5003600-5004600	Active TSS	NHLF	lung
46	chr6:5003600-5004800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:5003600-5004800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:5003600-5004800	Active TSS	H9 Cell Line	embryonic stem cell
49	chr6:5003600-5004800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:5003600-5004800	Active TSS	HUES48 Cell Line	embryonic stem cell

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