Variant report

Variant	rs1742485
Chromosome Location	chr6:80578610-80578611
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:80578460-80578610	HFF-Myc	foreskin:	n/a	n/a
2	RAD21	chr6:80577105-80580479	SK-N-SH	brain:	n/a	chr6:80578023-80578042 chr6:80579004-80579018 chr6:80579461-80579475 chr6:80579484-80579498 chr6:80578027-80578037 chr6:80579477-80579496
3	CTCF	chr6:80578480-80578630	SK-N-SH_RA	brain:	n/a	n/a
4	CTCF	chr6:80578560-80578710	AG10803	skin:	n/a	n/a
5	CTCF	chr6:80577346-80578651	SK-N-SH	brain:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:80578590-80578640	HNPCEpiC	eye:	n/a
2	chr6:80578590-80578640	AG04449	skin:	fetal
3	chr6:80578590-80578640	HEK293	kidney:	embryo
4	chr6:80578590-80578640	GM06990	blood:	n/a
5	chr6:80578590-80578640	HCPEpiC	choroid plexus:	n/a
6	chr6:80578590-80578640	RPTEC	kidney:	n/a
7	chr6:80578590-80578640	HCT-116	colon:	n/a
8	chr6:80578590-80578640	HL-60	blood:	n/a
9	chr6:80578590-80578640	CMK	blood:	n/a
10	chr6:80578590-80578640	ovcar-3	ovarian:	n/a
11	chr6:80578590-80578640	Caco-2	colon:	n/a
12	chr6:80578590-80578640	HCF	heart:	n/a
13	chr6:80578590-80578640	HepG2	liver:	n/a
14	chr6:80578590-80578640	H1-hESC	embryonic stem cell:	embryo
15	chr6:80578590-80578640	AG09319	gingival:	n/a
16	chr6:80578590-80578640	HCM	heart:	n/a
17	chr6:80578590-80578640	PrEC	prostate:	n/a
18	chr6:80578590-80578640	Jurkat	blood:	n/a
19	chr6:80578590-80578640	HRCEpiC	kidney:	n/a
20	chr6:80578590-80578640	ECC-1	luminal epithelium:	n/a
21	chr6:80578590-80578640	HEEpiC	esophagus:	n/a
22	chr6:80578590-80578640	Hela-S3	cervix:	n/a
23	chr6:80578590-80578640	AG09309	skin:	n/a
24	chr6:80578590-80578640	GM12892	blood:	n/a
25	chr6:80578590-80578640	GM19239	blood:	n/a
26	chr6:80578590-80578640	NB4	blood:	n/a
27	chr6:80578590-80578640	HRE	kidney:	n/a
28	chr6:80578590-80578640	AoSMC	blood vessel:	n/a
29	chr6:80578590-80578640	HPAEpiC	pulmonary alveolar:	n/a
30	chr6:80578590-80578640	T-47D	breast:	n/a
31	chr6:80578590-80578640	NT2-D1	testis:	n/a
32	chr6:80578590-80578640	SK-N-SH	brain:	n/a
33	chr6:80578590-80578640	SK-N-SH_RA	brain:	n/a
34	chr6:80578590-80578640	ProgFib	skin:	n/a
35	chr6:80578590-80578640	K562	blood:	n/a
36	chr6:80578590-80578640	IMR90	lung:	fetal
37	chr6:80578590-80578640	BJ	skin:	n/a
38	chr6:80578590-80578640	NH-A	brain:	n/a
39	chr6:80578590-80578640	PFSK-1	brain:	n/a
40	chr6:80578590-80578640	GM12878	blood:	n/a
41	chr6:80578590-80578640	PANC-1	pancreas:	n/a
42	chr6:80578590-80578640	SK-N-MC	brain:	n/a
43	chr6:80578590-80578640	AG10803	skin:	n/a
44	chr6:80578590-80578640	MCF-7	breast:	n/a
45	chr6:80578590-80578640	HRPEpiC	eye:	n/a
46	chr6:80578590-80578640	HIPEpiC	eye:	n/a
47	chr6:80578590-80578640	GM12891	blood:	n/a
48	chr6:80578590-80578640	NHBE	bronchial:	n/a
49	chr6:80578590-80578640	HAEpiC	amniotic membrane:	n/a
50	chr6:80578590-80578640	BE2_C	brain:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:80577908..80579667-chr6:80713971..80715630,2	K562	blood:
2	chr6:80577959..80580872-chr6:80588146..80590140,2	K562	blood:
3	chr6:80571013..80573087-chr6:80576802..80579710,2	K562	blood:

No data

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

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs180834	0.97[ASN][1000 genomes]
rs346279	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs346281	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs346282	0.86[ASN][1000 genomes]
rs346284	0.95[ASN][1000 genomes]
rs346286	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs346290	0.84[ASN][1000 genomes]
rs346291	0.86[ASN][1000 genomes]
rs346292	0.88[ASN][1000 genomes]
rs346299	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346301	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346302	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346303	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346304	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346307	0.86[MEX][hapmap]

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

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80576600-80582200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:80577400-80583400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:80577600-80579400	Enhancers	Dnd41	blood
4	chr6:80577600-80579800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:80577600-80580000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr6:80577600-80583200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:80577800-80579400	Enhancers	Ovary	ovary
8	chr6:80577800-80580000	Enhancers	Fetal Heart	heart
9	chr6:80577800-80580200	Enhancers	HMEC	breast
10	chr6:80578000-80579000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:80578000-80579000	Weak transcription	Fetal Stomach	stomach
12	chr6:80578000-80579200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:80578000-80579200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:80578000-80579200	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:80578000-80579200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:80578000-80579200	Weak transcription	Fetal Intestine Small	intestine
17	chr6:80578000-80579200	Weak transcription	Placenta	Placenta
18	chr6:80578000-80579200	Weak transcription	NHDF-Ad	bronchial
19	chr6:80578000-80579400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:80578000-80579400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:80578000-80579400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:80578000-80579400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:80578000-80579400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:80578000-80579400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:80578000-80579400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:80578000-80579400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr6:80578000-80579400	Weak transcription	Fetal Brain Female	brain
28	chr6:80578000-80579400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:80578000-80579400	Weak transcription	A549	lung
30	chr6:80578000-80579400	Weak transcription	Osteobl	bone
31	chr6:80578000-80579600	Enhancers	Liver	Liver
32	chr6:80578000-80579600	Weak transcription	Colon Smooth Muscle	Colon
33	chr6:80578000-80580000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:80578000-80582800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:80578200-80579200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr6:80578200-80579200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:80578200-80579200	Weak transcription	Hela-S3	cervix
38	chr6:80578200-80579400	Weak transcription	Adipose Nuclei	Adipose
39	chr6:80578200-80579400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr6:80578200-80579400	Weak transcription	Brain Substantia Nigra	brain
41	chr6:80578200-80579600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:80578400-80578800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr6:80578400-80578800	Weak transcription	HUVEC	blood vessel
44	chr6:80578400-80579000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:80578400-80579000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr6:80578400-80579000	Weak transcription	Fetal Muscle Leg	muscle
47	chr6:80578400-80579000	Enhancers	HepG2	liver
48	chr6:80578400-80579200	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr6:80578400-80579200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:80578400-80579200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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