Variant report

Variant	rs4925045
Chromosome Location	chr17:19619441-19619442
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:19619410-19619460	RPTEC	kidney:	n/a
2	chr17:19619410-19619460	SAEC	small airway:	n/a
3	chr17:19619410-19619460	NB4	blood:	n/a
4	chr17:19619410-19619460	HRCEpiC	kidney:	n/a
5	chr17:19619410-19619460	AG10803	skin:	n/a
6	chr17:19619410-19619460	HEK293	kidney:	embryo
7	chr17:19619410-19619460	HMEC	breast:	n/a
8	chr17:19619410-19619460	HCPEpiC	choroid plexus:	n/a
9	chr17:19619410-19619460	HNPCEpiC	eye:	n/a
10	chr17:19619410-19619460	SK-N-SH_RA	brain:	n/a
11	chr17:19619410-19619460	HPAEpiC	pulmonary alveolar:	n/a
12	chr17:19619410-19619460	SK-N-SH	brain:	n/a
13	chr17:19619410-19619460	HAEpiC	amniotic membrane:	n/a
14	chr17:19619410-19619460	Hepatocyte	liver:	n/a
15	chr17:19619410-19619460	GM19239	blood:	n/a
16	chr17:19619410-19619460	BJ	skin:	n/a
17	chr17:19619410-19619460	ProgFib	skin:	n/a
18	chr17:19619410-19619460	SK-N-MC	brain:	n/a
19	chr17:19619410-19619460	AoSMC	blood vessel:	n/a
20	chr17:19619410-19619460	H1-hESC	embryonic stem cell:	embryo
21	chr17:19619410-19619460	U87	brain:	n/a
22	chr17:19619410-19619460	GM06990	blood:	n/a
23	chr17:19619410-19619460	BE2_C	brain:	n/a
24	chr17:19619410-19619460	AG09309	skin:	n/a
25	chr17:19619410-19619460	HCT-116	colon:	n/a
26	chr17:19619410-19619460	NHDF-neo	bronchial:	n/a
27	chr17:19619410-19619460	HRPEpiC	eye:	n/a
28	chr17:19619410-19619460	PANC-1	pancreas:	n/a
29	chr17:19619410-19619460	ECC-1	luminal epithelium:	n/a
30	chr17:19619410-19619460	K562	blood:	n/a
31	chr17:19619410-19619460	PFSK-1	brain:	n/a
32	chr17:19619410-19619460	T-47D	breast:	n/a
33	chr17:19619410-19619460	MCF10A-Er-Src	breast:	n/a
34	chr17:19619410-19619460	NH-A	brain:	n/a
35	chr17:19619410-19619460	Hela-S3	cervix:	n/a
36	chr17:19619410-19619460	HL-60	blood:	n/a
37	chr17:19619410-19619460	HUVEC	blood vessel:	n/a
38	chr17:19619410-19619460	ovcar-3	ovarian:	n/a
39	chr17:19619410-19619460	HRE	kidney:	n/a
40	chr17:19619410-19619460	HIPEpiC	eye:	n/a
41	chr17:19619410-19619460	LNCaP	prostate:	n/a
42	chr17:19619410-19619460	Caco-2	colon:	n/a
43	chr17:19619410-19619460	HCF	heart:	n/a
44	chr17:19619410-19619460	IMR90	lung:	fetal
45	chr17:19619410-19619460	AG04449	skin:	fetal
46	chr17:19619410-19619460	GM12878	blood:	n/a
47	chr17:19619410-19619460	GM12891	blood:	n/a
48	chr17:19619410-19619460	PrEC	prostate:	n/a
49	chr17:19619410-19619460	AG09319	gingival:	n/a
50	chr17:19619410-19619460	GM12892	blood:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr17:19616686..19619985-chr17:19620299..19623719,4	MCF-7	breast:
2	chr17:19615883..19617829-chr17:19618251..19619755,2	MCF-7	breast:
3	chr17:19617555..19619828-chr17:19622180..19625084,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ALDH3A1-1	chr17:19619037-19622150	NONHSAT146520

No data

Variant related genes	Relation type
ENSG00000262681	CpG island
SLC47A2	CpG island
ENSG00000262681	Chromatin interaction
ENSG00000180638	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1006556	0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12451902	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12943590	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960360	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072327	0.89[JPT][hapmap]
rs2228100	0.90[JPT][hapmap]
rs35263947	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4646785	0.89[JPT][hapmap]
rs4924792	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs758426	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758427	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9897570	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9900497	0.83[CHB][hapmap];0.83[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	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv907866	chr17:19582533-19697976	Weak transcription Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv1807724	chr17:19597423-19656009	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv907867	chr17:19603060-19697976	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	esv1793043	chr17:19604821-19670329	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv526290	chr17:19613357-19651482	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19607200-19619800	Weak transcription	Spleen	Spleen
2	chr17:19607600-19627400	Weak transcription	Right Atrium	heart
3	chr17:19608800-19619800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr17:19611200-19619800	Weak transcription	Fetal Intestine Large	intestine
5	chr17:19612800-19619600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr17:19616200-19621400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr17:19617400-19619600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr17:19617600-19635400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr17:19618200-19620600	Weak transcription	Gastric	stomach
10	chr17:19618200-19623200	Weak transcription	Pancreas	Pancrea
11	chr17:19618400-19620000	Weak transcription	Fetal Intestine Small	intestine
12	chr17:19618400-19620600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr17:19618600-19620200	Active TSS	Brain Anterior Caudate	brain
14	chr17:19618600-19620200	Weak transcription	Stomach Mucosa	stomach
15	chr17:19618600-19620400	Weak transcription	Colonic Mucosa	Colon
16	chr17:19618800-19619600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr17:19619400-19619600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr17:19619400-19619600	Enhancers	HepG2	liver
19	chr17:19619400-19619600	Enhancers	HSMMtube	muscle
20	chr17:19619400-19620200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr17:19619400-19620600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:19619400-19620800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr17:19619400-19622200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr17:19619400-19622200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr17:19619400-19622400	Enhancers	A549	lung
26	chr17:19619400-19622800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr17:19619400-19624800	Enhancers	Esophagus	oesophagus
28	chr17:19619400-19625000	Enhancers	Fetal Muscle Leg	muscle

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