Variant report

Variant	rs12530996
Chromosome Location	chr7:97589975-97589976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr7:97589656-97589975	HepG2	liver:	n/a	chr7:97589847-97589858
2	POLR2A	chr7:97587562-97595221	MCF10A-Er-Src	breast:	n/a	n/a
3	TCF3	chr7:97589807-97590336	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:97589791-97589978	K562	blood:	n/a	n/a
5	POLR2A	chr7:97587702-97595211	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr7:97589463-97589992	Hela-S3	cervix:	n/a	n/a
7	PBX3	chr7:97589938-97590339	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
MIR5692A2	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12532137	0.88[ASN][1000 genomes]
rs34760117	0.88[ASN][1000 genomes]
rs35069412	0.96[ASN][1000 genomes]
rs55903636	0.96[ASN][1000 genomes]
rs6948093	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[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	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv428178	chr7:97402756-97648029	Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2758124	chr7:97476284-97648029	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2759546	chr7:97476284-97648029	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv1844775	chr7:97502740-97606178	Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
6	nsv970555	chr7:97502806-97639154	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
7	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
8	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12530996	AC004967.8	cis	Muscle Skeletal	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97558200-97592600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr7:97563600-97595200	Weak transcription	Lung	lung
3	chr7:97573800-97600200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr7:97574000-97600400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:97580000-97594000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr7:97581000-97597800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:97581800-97598400	Weak transcription	Gastric	stomach
8	chr7:97582800-97596800	Weak transcription	Pancreas	Pancrea
9	chr7:97582800-97600600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:97584400-97593800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:97584600-97592600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:97584600-97600800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:97586200-97599400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr7:97586400-97594600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr7:97589000-97594400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr7:97589000-97595800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:97589200-97593200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr7:97589200-97594000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr7:97589200-97594400	Weak transcription	Spleen	Spleen
20	chr7:97589200-97595000	Weak transcription	Brain Angular Gyrus	brain

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