Variant report

Variant	rs6503885
Chromosome Location	chr17:45930112-45930113
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:45929492-45930416	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr17:45929685-45930302	SK-N-SH	brain:	n/a	n/a
3	GATA2	chr17:45929723-45930148	SH-SY5Y	brain:	n/a	n/a
4	POLR2A	chr17:45929708-45930263	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr17:45929125-45930569	H1-neurons	neurons:	n/a	n/a
6	GATA3	chr17:45929984-45930184	SH-SY5Y	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:45930106-45930156	SK-N-SH	brain:	n/a
2	chr17:45930106-45930156	IMR90	lung:	fetal
3	chr17:45930106-45930156	ECC-1	luminal epithelium:	n/a
4	chr17:45930106-45930156	AG09319	gingival:	n/a
5	chr17:45930106-45930156	HPAEpiC	pulmonary alveolar:	n/a
6	chr17:45930106-45930156	SAEC	small airway:	n/a
7	chr17:45930106-45930156	H1-hESC	embryonic stem cell:	embryo
8	chr17:45930106-45930156	GM12891	blood:	n/a
9	chr17:45930106-45930156	HCT-116	colon:	n/a
10	chr17:45930106-45930156	PFSK-1	brain:	n/a
11	chr17:45930106-45930156	Jurkat	blood:	n/a
12	chr17:45930106-45930156	HEK293	kidney:	embryo
13	chr17:45930106-45930156	HRCEpiC	kidney:	n/a
14	chr17:45930106-45930156	AG09309	skin:	n/a
15	chr17:45930106-45930156	HRE	kidney:	n/a
16	chr17:45930106-45930156	HIPEpiC	eye:	n/a
17	chr17:45930106-45930156	HNPCEpiC	eye:	n/a
18	chr17:45930106-45930156	SKMC	muscle:	n/a
19	chr17:45930106-45930156	AG04449	skin:	fetal
20	chr17:45930106-45930156	BJ	skin:	n/a
21	chr17:45930106-45930156	GM12878	blood:	n/a
22	chr17:45930106-45930156	HEEpiC	esophagus:	n/a
23	chr17:45930106-45930156	SK-N-SH_RA	brain:	n/a
24	chr17:45930106-45930156	BE2_C	brain:	n/a
25	chr17:45930106-45930156	GM12892	blood:	n/a
26	chr17:45930106-45930156	U87	brain:	n/a
27	chr17:45930106-45930156	GM19239	blood:	n/a
28	chr17:45930106-45930156	MCF-7	breast:	n/a
29	chr17:45930106-45930156	SK-N-MC	brain:	n/a
30	chr17:45930106-45930156	GM06990	blood:	n/a
31	chr17:45930106-45930156	LNCaP	prostate:	n/a
32	chr17:45930106-45930156	HMEC	breast:	n/a
33	chr17:45930106-45930156	NHBE	bronchial:	n/a
34	chr17:45930106-45930156	AG10803	skin:	n/a
35	chr17:45930106-45930156	Hepatocyte	liver:	n/a
36	chr17:45930106-45930156	K562	blood:	n/a
37	chr17:45930106-45930156	HepG2	liver:	n/a
38	chr17:45930106-45930156	AG04450	lung:	fetal
39	chr17:45930106-45930156	HAEpiC	amniotic membrane:	n/a
40	chr17:45930106-45930156	PrEC	prostate:	n/a
41	chr17:45930106-45930156	PANC-1	pancreas:	n/a
42	chr17:45930106-45930156	HCM	heart:	n/a
43	chr17:45930106-45930156	HL-60	blood:	n/a
44	chr17:45930106-45930156	RPTEC	kidney:	n/a
45	chr17:45930106-45930156	Hela-S3	cervix:	n/a
46	chr17:45930106-45930156	HCF	heart:	n/a
47	chr17:45930106-45930156	CMK	blood:	n/a
48	chr17:45930106-45930156	ovcar-3	ovarian:	n/a
49	chr17:45930106-45930156	Caco-2	colon:	n/a
50	chr17:45930106-45930156	HUVEC	blood vessel:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45928961..45933138-chr17:45960892..45963467,3	K562	blood:
2	chr17:45921031..45932631-chr17:45970978..45975136,16	K562	blood:
3	chr17:45928850..45930934-chr17:46029439..46031345,2	K562	blood:
4	chr17:45927380..45931249-chr17:45931939..45938449,12	K562	blood:
5	chr17:45925951..45927687-chr17:45928711..45930678,2	K562	blood:
6	chr17:45927036..45931880-chr17:45931939..45936922,11	K562	blood:
7	chr17:45928921..45932195-chr17:46017729..46021262,3	MCF-7	breast:
8	chr17:45907387..45909991-chr17:45928355..45930503,2	MCF-7	breast:
9	chr17:45929322..45931264-chr17:45947202..45949879,3	K562	blood:
10	chr17:45923146..45930414-chr17:45970842..45976007,11	MCF-7	breast:
11	chr17:45928046..45933138-chr17:45958246..45966286,8	K562	blood:

No data

Variant related genes	Relation type
SP6	TF binding region
SP6	CpG island
ENSG00000159111	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000266821	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000141294	Chromatin interaction
ENSG00000234494	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs16948835	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2875737	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55919794	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62066131	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62076141	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72833458	0.89[ASN][1000 genomes]
rs8080650	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908573	chr17:45858487-45956073	Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv908574	chr17:45876022-45930584	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv517880	chr17:45887951-45933341	Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6503885	LRRC46	cis	Thyroid	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45927600-45930200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
2	chr17:45927600-45930200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
3	chr17:45928200-45930200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr17:45928400-45930200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
5	chr17:45928400-45931400	Bivalent Enhancer	Fetal Muscle Leg	muscle
6	chr17:45928400-45931400	Enhancers	Lung	lung
7	chr17:45929200-45930200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
8	chr17:45929200-45930400	Flanking Active TSS	K562	blood
9	chr17:45929400-45930200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
10	chr17:45929400-45930200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
11	chr17:45929600-45930200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr17:45929600-45930200	Bivalent Enhancer	Fetal Kidney	kidney
13	chr17:45929600-45931200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr17:45929800-45930200	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
15	chr17:45929800-45930200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
16	chr17:45929800-45930200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr17:45929800-45930400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr17:45929800-45930400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr17:45929800-45940000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr17:45930000-45930200	Flanking Bivalent TSS/Enh	ES-WA7 Cell Line	embryonic stem cell
21	chr17:45930000-45930200	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
22	chr17:45930000-45930200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
23	chr17:45930000-45930200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
24	chr17:45930000-45930200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr17:45930000-45931000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr17:45930000-45931000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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