Variant report

Variant	rs12706413
Chromosome Location	chr7:122075328-122075329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10235626	0.85[CEU][hapmap]
rs10238269	0.82[CEU][hapmap]
rs10246078	0.85[CEU][hapmap]
rs10264820	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs10269374	0.85[CEU][hapmap]
rs11973627	1.00[GIH][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11984390	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12706410	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706411	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706412	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706415	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13222975	0.85[CEU][hapmap]
rs13231250	0.89[AMR][1000 genomes]
rs13238360	0.85[CEU][hapmap];0.89[AMR][1000 genomes]
rs13239116	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13241783	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17380636	0.85[CEU][hapmap]
rs17463779	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17463849	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28406245	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492775	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34252702	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34565849	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35090045	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35168749	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35636140	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35710523	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35760934	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947220	0.85[CEU][hapmap]
rs6955734	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs6980172	0.85[CEU][hapmap]
rs71571077	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71573096	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71573097	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656294	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017029	chr7:121958574-122338623	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12706413	SNX7	trans	lymphoblastoid	seeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:122013800-122081800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr7:122022400-122095000	Weak transcription	Gastric	stomach
3	chr7:122047000-122155400	Weak transcription	Left Ventricle	heart
4	chr7:122056200-122122200	Weak transcription	Liver	Liver
5	chr7:122061200-122095200	Weak transcription	Aorta	Aorta
6	chr7:122069000-122078400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:122071400-122076400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr7:122071600-122076400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:122071600-122076600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:122071800-122076600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr7:122071800-122078000	Weak transcription	Brain Germinal Matrix	brain
12	chr7:122072200-122076200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:122072600-122077000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr7:122074000-122078000	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr7:122074200-122076600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:122074400-122076000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:122074600-122076200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:122074600-122076200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:122074600-122076600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:122074600-122076600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr7:122074800-122075800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr7:122074800-122076200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr7:122074800-122078200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr7:122074800-122078400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:122074800-122078400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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