Variant report

Variant	rs34834489
Chromosome Location	chr17:19620264-19620265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr17:19619471-19620389	ECC-1	luminal epithelium:	n/a	chr17:19620217-19620232
2	ESR1	chr17:19619536-19620462	ECC-1	luminal epithelium:	n/a	chr17:19620217-19620232
3	MAX	chr17:19619615-19620280	ECC-1	luminal epithelium:	n/a	n/a
4	EP300	chr17:19619506-19620555	ECC-1	luminal epithelium:	n/a	n/a
5	EP300	chr17:19619524-19620376	ECC-1	luminal epithelium:	n/a	n/a
6	TCF12	chr17:19619479-19621400	ECC-1	luminal epithelium:	n/a	chr17:19619595-19619605
7	TCF12	chr17:19619472-19621437	ECC-1	luminal epithelium:	n/a	chr17:19619595-19619605
8	ESR1	chr17:19619582-19620346	ECC-1	luminal epithelium:	n/a	chr17:19620217-19620232
9	NFIC	chr17:19619616-19620388	ECC-1	luminal epithelium:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:19620263-19620313	U87	brain:	n/a
2	chr17:19620263-19620313	AG09319	gingival:	n/a
3	chr17:19620263-19620313	HRCEpiC	kidney:	n/a
4	chr17:19620263-19620313	IMR90	lung:	fetal
5	chr17:19620263-19620313	HPAEpiC	pulmonary alveolar:	n/a
6	chr17:19620263-19620313	HCF	heart:	n/a
7	chr17:19620263-19620313	BE2_C	brain:	n/a
8	chr17:19620263-19620313	ProgFib	skin:	n/a
9	chr17:19620263-19620313	Caco-2	colon:	n/a
10	chr17:19620263-19620313	Hepatocyte	liver:	n/a
11	chr17:19620263-19620313	PFSK-1	brain:	n/a
12	chr17:19620263-19620313	RPTEC	kidney:	n/a
13	chr17:19620263-19620313	HEEpiC	esophagus:	n/a
14	chr17:19620263-19620313	Hela-S3	cervix:	n/a
15	chr17:19620263-19620313	Jurkat	blood:	n/a
16	chr17:19620263-19620313	HNPCEpiC	eye:	n/a
17	chr17:19620263-19620313	BJ	skin:	n/a
18	chr17:19620263-19620313	GM06990	blood:	n/a
19	chr17:19620263-19620313	AG09309	skin:	n/a
20	chr17:19620263-19620313	HAEpiC	amniotic membrane:	n/a
21	chr17:19620263-19620313	K562	blood:	n/a
22	chr17:19620263-19620313	NHDF-neo	bronchial:	n/a
23	chr17:19620263-19620313	HRPEpiC	eye:	n/a
24	chr17:19620263-19620313	HMEC	breast:	n/a
25	chr17:19620263-19620313	HCM	heart:	n/a
26	chr17:19620263-19620313	GM12878	blood:	n/a
27	chr17:19620263-19620313	SAEC	small airway:	n/a
28	chr17:19620263-19620313	CMK	blood:	n/a
29	chr17:19620263-19620313	PANC-1	pancreas:	n/a
30	chr17:19620263-19620313	GM19239	blood:	n/a
31	chr17:19620263-19620313	NH-A	brain:	n/a
32	chr17:19620263-19620313	LNCaP	prostate:	n/a
33	chr17:19620263-19620313	HRE	kidney:	n/a
34	chr17:19620263-19620313	GM12891	blood:	n/a
35	chr17:19620263-19620313	ECC-1	luminal epithelium:	n/a
36	chr17:19620263-19620313	AG04450	lung:	fetal
37	chr17:19620263-19620313	MCF10A-Er-Src	breast:	n/a
38	chr17:19620263-19620313	T-47D	breast:	n/a
39	chr17:19620263-19620313	HIPEpiC	eye:	n/a
40	chr17:19620263-19620313	AG10803	skin:	n/a
41	chr17:19620263-19620313	NT2-D1	testis:	n/a
42	chr17:19620263-19620313	GM12892	blood:	n/a
43	chr17:19620263-19620313	HUVEC	blood vessel:	n/a
44	chr17:19620263-19620313	NHBE	bronchial:	n/a
45	chr17:19620263-19620313	AG04449	skin:	fetal
46	chr17:19620263-19620313	SK-N-MC	brain:	n/a
47	chr17:19620263-19620313	H1-hESC	embryonic stem cell:	embryo
48	chr17:19620263-19620313	A549	lung:	n/a
49	chr17:19620263-19620313	AoSMC	blood vessel:	n/a
50	chr17:19620263-19620313	HCPEpiC	choroid plexus:	n/a

No data

(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
SLC47A2	TF binding region
ENSG00000262681	TF binding region
ENSG00000262681	CpG island
SLC47A2	CpG island

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11204410	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11655302	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11655457	0.81[ASN][1000 genomes]
rs11655989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11656096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11657205	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12601430	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12945000	0.81[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34834489	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19607600-19627400	Weak transcription	Right Atrium	heart
2	chr17:19616200-19621400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:19617600-19635400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr17:19618200-19620600	Weak transcription	Gastric	stomach
5	chr17:19618200-19623200	Weak transcription	Pancreas	Pancrea
6	chr17:19618400-19620600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr17:19618600-19620400	Weak transcription	Colonic Mucosa	Colon
8	chr17:19619400-19620600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr17:19619400-19620800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr17:19619400-19622200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr17:19619400-19622200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr17:19619400-19622400	Enhancers	A549	lung
13	chr17:19619400-19622800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr17:19619400-19624800	Enhancers	Esophagus	oesophagus
15	chr17:19619400-19625000	Enhancers	Fetal Muscle Leg	muscle
16	chr17:19619600-19620400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr17:19619600-19620400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr17:19619600-19621600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr17:19619600-19621800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr17:19619600-19622200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr17:19619600-19622200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr17:19619600-19625000	Enhancers	HMEC	breast
23	chr17:19619800-19622000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr17:19619800-19622000	Enhancers	NHEK	skin
25	chr17:19619800-19627800	Enhancers	Fetal Intestine Large	intestine
26	chr17:19620000-19620400	Weak transcription	Spleen	Spleen
27	chr17:19620000-19621200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr17:19620000-19624800	Enhancers	HSMMtube	muscle
29	chr17:19620000-19628000	Enhancers	Fetal Intestine Small	intestine
30	chr17:19620200-19620600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr17:19620200-19620600	Enhancers	Brain Anterior Caudate	brain
32	chr17:19620200-19621200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr17:19620200-19621400	Bivalent Enhancer	HepG2	liver
34	chr17:19620200-19624800	Enhancers	Stomach Mucosa	stomach

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