Variant report

Variant	rs7399127
Chromosome Location	chr12:122039802-122039803
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10770182	0.82[AMR][1000 genomes]
rs10770191	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840649	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12320939	0.94[ASW][hapmap];0.85[CEU][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs2669163	0.81[CEU][hapmap]
rs2669166	0.88[ASW][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs2669168	0.81[CEU][hapmap]
rs2720022	0.88[ASW][hapmap];0.81[CEU][hapmap];0.96[MEX][hapmap]
rs2720041	0.84[MEX][hapmap]
rs28409019	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28651135	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28679490	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28758358	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2942368	0.88[ASW][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap]
rs2942379	0.88[ASW][hapmap];0.96[MEX][hapmap]
rs3825175	0.94[ASW][hapmap];0.82[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs3934658	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300349	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7397776	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7398628	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925531	0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7399127	GTF2H3	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122020800-122040400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:122028600-122048000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr12:122028600-122048400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:122028800-122048400	Weak transcription	Brain Angular Gyrus	brain
5	chr12:122028800-122049000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:122028800-122064000	Weak transcription	Right Atrium	heart
7	chr12:122029200-122049800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:122033200-122049600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:122033400-122041600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:122033800-122049600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:122034000-122046400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:122034000-122048400	Weak transcription	Brain Anterior Caudate	brain
13	chr12:122034600-122048400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:122034800-122040400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:122035000-122048000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:122035000-122048200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:122036000-122041000	Enhancers	Fetal Intestine Small	intestine
18	chr12:122036400-122048000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:122036600-122040400	Weak transcription	Colonic Mucosa	Colon
20	chr12:122037200-122040200	Weak transcription	Gastric	stomach
21	chr12:122037200-122047400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr12:122038600-122041200	Enhancers	Fetal Intestine Large	intestine
23	chr12:122038600-122048000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:122039000-122048000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:122039200-122040400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:122039200-122048400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:122039400-122040400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr12:122039600-122047600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr12:122039800-122040200	Weak transcription	Stomach Mucosa	stomach
30	chr12:122039800-122040400	Weak transcription	Fetal Muscle Leg	muscle

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