Variant report

Variant	rs546520
Chromosome Location	chr6:13299462-13299463
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:13299403-13299482	HUVEC	blood vessel:	n/a	n/a
2	PAX5	chr6:13299430-13299673	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:13253507..13255160-chr6:13298362..13301055,2	K562	blood:
2	chr6:13298717..13301545-chr6:13301638..13304448,3	K562	blood:
3	chr6:13274083..13277421-chr6:13297082..13301885,5	K562	blood:
4	chr6:13296819..13300441-chr6:13305761..13308537,4	K562	blood:
5	chr6:13274184..13276021-chr6:13298954..13301885,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000215022	TF binding region
ENSG00000215022	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12203576	0.91[ASN][1000 genomes]
rs1899262	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs202020	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439538	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439546	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2496141	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2496143	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2496155	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs364884	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381134	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846903	0.81[ASN][1000 genomes]
rs408639	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs408923	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs446843	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570338	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs641293	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910418	0.81[AMR][1000 genomes]
rs7774863	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs878698	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9381915	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9473896	0.87[ASN][1000 genomes]
rs9473901	0.89[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv10875	chr6:13298917-13300100	Strong transcription Genic enhancers Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs546520	RP1-257A7.5	cis	Thyroid	GTEx
rs546520	PHACTR1	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
2	chr6:13285400-13302400	Weak transcription	HUVEC	blood vessel
3	chr6:13287000-13303600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:13288400-13302600	Weak transcription	Hela-S3	cervix
5	chr6:13288400-13302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:13288600-13302400	Strong transcription	Fetal Brain Female	brain
7	chr6:13288600-13302600	Strong transcription	Fetal Muscle Leg	muscle
8	chr6:13288600-13321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:13288600-13326400	Strong transcription	Primary T cells from cord blood	blood
10	chr6:13289000-13299800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:13289800-13327000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:13290200-13302800	Weak transcription	NHEK	skin
13	chr6:13290400-13310400	Strong transcription	Dnd41	blood
14	chr6:13290600-13302800	Weak transcription	Stomach Mucosa	stomach
15	chr6:13291000-13302800	Strong transcription	Fetal Stomach	stomach
16	chr6:13291200-13303000	Strong transcription	Fetal Intestine Small	intestine
17	chr6:13291200-13310400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr6:13291400-13299600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr6:13291400-13300200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:13291400-13303600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:13291600-13300800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr6:13291600-13302400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:13291600-13302400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:13291600-13302600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:13291600-13302600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr6:13291600-13305800	Strong transcription	Thymus	Thymus
27	chr6:13291800-13301800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:13291800-13320400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr6:13292000-13302600	Strong transcription	Fetal Intestine Large	intestine
30	chr6:13292000-13326000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:13292400-13299800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:13292400-13302600	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr6:13292600-13326600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:13293000-13302800	Strong transcription	Fetal Lung	lung
35	chr6:13293200-13305400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:13294200-13302600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:13294600-13301200	Weak transcription	Brain Angular Gyrus	brain
38	chr6:13295000-13300600	Weak transcription	NH-A	brain
39	chr6:13295000-13304800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr6:13295200-13302200	Weak transcription	NHDF-Ad	bronchial
41	chr6:13295200-13305200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:13295400-13300200	Weak transcription	K562	blood
43	chr6:13295400-13302000	Weak transcription	Fetal Brain Male	brain
44	chr6:13295400-13302600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:13295600-13300200	Weak transcription	HSMMtube	muscle
46	chr6:13295600-13301200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr6:13295600-13302600	Weak transcription	Esophagus	oesophagus
48	chr6:13295600-13302800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:13295800-13299800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:13295800-13301400	Weak transcription	Brain Cingulate Gyrus	brain

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