Variant report

Variant	rs2215955
Chromosome Location	chr7:38469039-38469040
allele	A/C
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	CTCF	chr7:38469020-38469170	GM06990	blood:	n/a	n/a

Variant related genes	Relation type
AMPH	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10244280	0.87[ASN][1000 genomes]
rs10247761	0.83[EUR][1000 genomes]
rs10269686	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10281867	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2267806	0.84[CHD][hapmap]
rs2267807	0.83[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs2284253	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2893559	0.80[EUR][1000 genomes]
rs7782361	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758112	chr7:38218703-38523455	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv2759524	chr7:38218703-38523455	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv427776	chr7:38218703-38523455	Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1025974	chr7:38227528-38503472	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv538819	chr7:38227528-38503472	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv1020990	chr7:38257707-38503472	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv1019941	chr7:38319437-38472680	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	nsv1031936	chr7:38319437-38503472	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv429745	chr7:38323485-38470561	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription 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	30 gene(s)	inside rSNPs	diseases
11	nsv830965	chr7:38350614-38521047	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv830966	chr7:38393663-38602553	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv887964	chr7:38457144-38501065	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv1825425	chr7:38457144-38507180	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2215955	TBX20	cis	parietal	SCAN
rs2215955	AMPH	cis	cerebellar cortex	BrainEAC
rs2215955	AMPH	cis	brain	BrainEAC

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38431600-38489000	Weak transcription	Brain Angular Gyrus	brain
2	chr7:38439000-38483000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:38456200-38481400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr7:38457400-38479600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr7:38459000-38473400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:38459200-38470400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr7:38467200-38469400	Enhancers	Primary T cells from cord blood	blood
8	chr7:38467600-38472800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr7:38467800-38472400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:38467800-38472600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr7:38467800-38472600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr7:38467800-38472800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr7:38467800-38495600	Weak transcription	Aorta	Aorta
14	chr7:38468200-38475000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:38468400-38472400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:38468400-38480800	Weak transcription	Fetal Brain Female	brain
17	chr7:38468400-38492000	Weak transcription	Fetal Heart	heart
18	chr7:38468600-38469200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:38468600-38469200	Strong transcription	Fetal Stomach	stomach
20	chr7:38468600-38469200	Enhancers	Fetal Thymus	thymus
21	chr7:38468800-38472800	Weak transcription	Thymus	Thymus
22	chr7:38468800-38473400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:38469000-38477000	Weak transcription	Fetal Brain Male	brain

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