Variant report

Variant	rs320683
Chromosome Location	chr7:137039328-137039329
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	NFIC	chr7:137039016-137039621	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000228031	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1367593	0.87[EUR][1000 genomes]
rs161340	0.88[EUR][1000 genomes]
rs161341	0.88[EUR][1000 genomes]
rs161342	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs161345	0.87[EUR][1000 genomes]
rs167668	0.87[EUR][1000 genomes]
rs1731951	0.80[CEU][hapmap];0.82[JPT][hapmap]
rs178612	0.88[EUR][1000 genomes]
rs192935	0.88[EUR][1000 genomes]
rs192936	0.87[EUR][1000 genomes]
rs2599356	0.87[EUR][1000 genomes]
rs320684	0.87[EUR][1000 genomes]
rs320686	0.84[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs320687	0.88[EUR][1000 genomes]
rs320689	0.86[EUR][1000 genomes]
rs320690	0.87[EUR][1000 genomes]
rs320691	0.87[EUR][1000 genomes]
rs320692	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs320693	0.87[EUR][1000 genomes]
rs320694	0.87[EUR][1000 genomes]
rs320695	0.87[EUR][1000 genomes]
rs320697	0.87[EUR][1000 genomes]
rs725838	0.87[EUR][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	nsv1029192	chr7:136433278-137147566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869820	chr7:136990386-137347718	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1027868	chr7:137004690-137311653	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv539134	chr7:137004690-137311653	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv889242	chr7:137005808-137081223	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs320683	AC078842.3	cis	Thyroid	GTEx
rs320683	PTN	cis	Nerve Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:137036200-137040200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr7:137037200-137039400	Enhancers	Rectal Smooth Muscle	rectum
3	chr7:137037200-137040400	Enhancers	Brain Germinal Matrix	brain
4	chr7:137037600-137040200	Enhancers	Fetal Lung	lung
5	chr7:137037800-137045800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:137038600-137039400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr7:137038600-137039400	Enhancers	Stomach Smooth Muscle	stomach
8	chr7:137038600-137039600	Active TSS	Brain Angular Gyrus	brain
9	chr7:137038600-137039800	Enhancers	Fetal Heart	heart
10	chr7:137038600-137040000	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr7:137038600-137040000	Enhancers	Fetal Stomach	stomach
12	chr7:137039000-137039400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
13	chr7:137039000-137039600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr7:137039000-137039600	Enhancers	Ovary	ovary
15	chr7:137039000-137039600	Enhancers	NH-A	brain
16	chr7:137039000-137040000	Enhancers	Colon Smooth Muscle	Colon
17	chr7:137039200-137039400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr7:137039200-137039400	Flanking Active TSS	Brain Substantia Nigra	brain
19	chr7:137039200-137039400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr7:137039200-137039600	Flanking Active TSS	Brain Anterior Caudate	brain
21	chr7:137039200-137039600	Active TSS	Brain Cingulate Gyrus	brain
22	chr7:137039200-137039600	Enhancers	Esophagus	oesophagus
23	chr7:137039200-137039600	Enhancers	Fetal Muscle Leg	muscle
24	chr7:137039200-137040000	Active TSS	Cortex derived primary cultured neurospheres	brain

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