Variant report

Variant	rs1655882
Chromosome Location	chr6:80578095-80578096
allele	A/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	TAL1	chr6:80577815-80578156	K562	blood:	n/a	n/a
2	CTCF	chr6:80577960-80578110	NHLF	lung:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
3	CTCF	chr6:80577802-80578245	IMR90	lung:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
4	RAD21	chr6:80577737-80578305	HCT-116	colon:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
5	MAZ	chr6:80577893-80578149	GM12878	blood:	n/a	n/a
6	SMC3	chr6:80577905-80578182	HepG2	liver:	n/a	chr6:80578027-80578041 chr6:80578027-80578037
7	CTCF	chr6:80577960-80578110	NHDF-neo	bronchial:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
8	RAD21	chr6:80577846-80578174	HepG2	liver:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
9	CTCF	chr6:80577851-80578145	HepG2	liver:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
10	CTCF	chr6:80577960-80578110	AG04450	lung:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
11	CTCF	chr6:80577771-80578255	A549	lung:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
12	CTCF	chr6:80577896-80578158	T-47D	breast:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
13	RAD21	chr6:80577920-80578118	K562	blood:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
14	CTCF	chr6:80577960-80578110	HMEC	breast:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
15	CTCF	chr6:80577732-80578360	HCT-116	colon:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
16	BHLHE40	chr6:80577908-80578146	GM12878	blood:	n/a	n/a
17	YY1	chr6:80577939-80578214	GM12878	blood:	n/a	n/a
18	CTCF	chr6:80577980-80578130	HRE	kidney:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
19	MYC	chr6:80577973-80578173	MCF10A-Er-Src	breast:	n/a	n/a
20	CTCF	chr6:80577903-80578168	K562	blood:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
21	CTCF	chr6:80577960-80578110	HRE	kidney:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
22	CTCF	chr6:80577826-80578257	GM12878	blood:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
23	RAD21	chr6:80577625-80578394	HCT-116	colon:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
24	CTCF	chr6:80577960-80578110	HCPEpiC	choroid plexus:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
25	CTCF	chr6:80577960-80578110	GM12878	blood:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
26	CTCF	chr6:80577960-80578110	AG09309	skin:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
27	CTCF	chr6:80577984-80578120	Fibrobl	skin:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
28	CTCF	chr6:80578000-80578150	GM12869	blood:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
29	CTCF	chr6:80577877-80578158	A549	lung:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
30	RAD21	chr6:80577778-80578272	H1-hESC	embryonic stem cell:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
31	IRF3	chr6:80577981-80578116	GM12878	blood:	n/a	n/a
32	CTCF	chr6:80577805-80578162	H1-hESC	embryonic stem cell:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
33	CTCF	chr6:80577814-80578135	SK-N-SH_RA	brain:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
34	CTCF	chr6:80577785-80578199	ECC-1	luminal epithelium:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
35	RAD21	chr6:80577642-80578338	MCF-7	breast:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
36	CTCF	chr6:80578020-80578170	HEK293	kidney:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
37	FOS	chr6:80577934-80578148	MCF10A-Er-Src	breast:	n/a	n/a
38	ZNF384	chr6:80577857-80578292	GM12878	blood:	n/a	n/a
39	CTCF	chr6:80577612-80578480	A549	lung:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
40	CREB1	chr6:80577840-80578158	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr6:80577980-80578130	Caco-2	colon:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
42	CTCF	chr6:80578060-80578106	GM12892	blood:	n/a	n/a
43	MAX	chr6:80577920-80578521	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr6:80577960-80578110	SK-N-SH_RA	brain:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
45	RAD21	chr6:80577740-80578306	ECC-1	luminal epithelium:	n/a	chr6:80578023-80578042 chr6:80578027-80578037
46	SMC3	chr6:80577850-80578210	K562	blood:	n/a	chr6:80578027-80578041 chr6:80578027-80578037
47	CTCF	chr6:80577960-80578110	HPAF	blood vessel:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
48	CTCF	chr6:80577827-80578330	MCF-7	breast:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
49	CTCF	chr6:80577960-80578110	HMF	breast:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
50	CTCF	chr6:80577864-80578153	Hela-S3	cervix:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043

No.	Distal block	Cell Line	Cell type
1	chr6:80280197..80280802-chr6:80577120..80578118,2	MCF-7	breast:
2	chr6:80423120..80423711-chr6:80577789..80578553,2	K562	blood:
3	chr6:80577908..80579667-chr6:80713971..80715630,2	K562	blood:
4	chr6:80487640..80488609-chr6:80577520..80578268,3	MCF-7	breast:
5	chr6:80487449..80488333-chr6:80577575..80578144,3	MCF-7	breast:
6	chr6:80487430..80488393-chr6:80577490..80578546,7	K562	blood:
7	chr6:80564754..80565348-chr6:80577673..80578339,2	MCF-7	breast:
8	chr6:80577959..80580872-chr6:80588146..80590140,2	K562	blood:
9	chr6:80571013..80573087-chr6:80576802..80579710,2	K562	blood:

Variant related genes	Relation type
ENSG00000233835	TF binding region
ENSG00000112742	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1010938	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11752625	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11754406	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1321841	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1321842	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1321843	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1321844	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7775834	0.88[AMR][1000 genomes];0.85[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	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats 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
3	nsv1021143	chr6:80400195-80598163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	esv3693359	chr6:80539454-80606537	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1655882	TPBG	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80571000-80578200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:80575400-80578200	Weak transcription	Pancreas	Pancrea
3	chr6:80576600-80582200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:80577400-80583400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:80577600-80578200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:80577600-80578400	Flanking Active TSS	Brain Anterior Caudate	brain
7	chr6:80577600-80578400	Enhancers	Fetal Intestine Large	intestine
8	chr6:80577600-80579400	Enhancers	Dnd41	blood
9	chr6:80577600-80579800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:80577600-80580000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr6:80577600-80583200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:80577800-80578200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:80577800-80578200	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr6:80577800-80578200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr6:80577800-80578200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr6:80577800-80578200	Enhancers	Adipose Nuclei	Adipose
17	chr6:80577800-80578200	Active TSS	Brain Angular Gyrus	brain
18	chr6:80577800-80578200	Enhancers	Brain Substantia Nigra	brain
19	chr6:80577800-80578400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr6:80577800-80578400	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr6:80577800-80578400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:80577800-80578400	Enhancers	Brain Germinal Matrix	brain
23	chr6:80577800-80578400	Enhancers	Fetal Muscle Leg	muscle
24	chr6:80577800-80578400	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr6:80577800-80578400	Enhancers	Stomach Mucosa	stomach
26	chr6:80577800-80578400	Enhancers	K562	blood
27	chr6:80577800-80578600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr6:80577800-80578600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr6:80577800-80578600	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr6:80577800-80578600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:80577800-80578600	Enhancers	Fetal Thymus	thymus
32	chr6:80577800-80579400	Enhancers	Ovary	ovary
33	chr6:80577800-80580000	Enhancers	Fetal Heart	heart
34	chr6:80577800-80580200	Enhancers	HMEC	breast
35	chr6:80578000-80578200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr6:80578000-80578200	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr6:80578000-80578200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:80578000-80578200	Active TSS	Brain Cingulate Gyrus	brain
39	chr6:80578000-80578200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr6:80578000-80578200	Enhancers	Hela-S3	cervix
41	chr6:80578000-80578200	Enhancers	NHEK	skin
42	chr6:80578000-80578400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:80578000-80578400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:80578000-80578400	Enhancers	Fetal Brain Male	brain
45	chr6:80578000-80578400	Enhancers	HUVEC	blood vessel
46	chr6:80578000-80578600	Enhancers	Primary T cells fromperipheralblood	blood
47	chr6:80578000-80579000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:80578000-80579000	Weak transcription	Fetal Stomach	stomach
49	chr6:80578000-80579200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr6:80578000-80579200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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