Variant report

Variant	rs12451902
Chromosome Location	chr17:19619063-19619064
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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:

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

Variant related genes	Relation type
ENSG00000262681	Chromatin interaction
ENSG00000180638	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1006556	0.82[ASN][1000 genomes]
rs12943590	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960360	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35263947	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924792	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925045	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758426	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758427	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9897570	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9900497	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:23 , 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	chr17:19610600-19619400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr17:19610800-19619400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr17:19611000-19619400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr17:19611200-19619800	Weak transcription	Fetal Intestine Large	intestine
8	chr17:19612800-19619600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr17:19616200-19621400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr17:19617200-19619400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr17:19617400-19619600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr17:19617600-19635400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr17:19618200-19619400	Weak transcription	Esophagus	oesophagus
14	chr17:19618200-19619400	Weak transcription	Fetal Muscle Leg	muscle
15	chr17:19618200-19619400	Weak transcription	HepG2	liver
16	chr17:19618200-19620600	Weak transcription	Gastric	stomach
17	chr17:19618200-19623200	Weak transcription	Pancreas	Pancrea
18	chr17:19618400-19620000	Weak transcription	Fetal Intestine Small	intestine
19	chr17:19618400-19620600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr17:19618600-19620200	Active TSS	Brain Anterior Caudate	brain
21	chr17:19618600-19620200	Weak transcription	Stomach Mucosa	stomach
22	chr17:19618600-19620400	Weak transcription	Colonic Mucosa	Colon
23	chr17:19618800-19619600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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