Variant report

Variant	rs3934658
Chromosome Location	chr12:122037099-122037100
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122036694..122038396-chr12:122040924..122043659,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252393	Chromatin interaction

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	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840649	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[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	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28651135	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28679490	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28758358	0.98[AMR][1000 genomes];0.97[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]
rs7300349	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7397776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7398628	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7399127	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]
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
rs3934658	GTF2H3	cis	cerebellum	SCAN

Chromatin state (count:47 , 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	chr12:122028200-122038800	Weak transcription	Pancreas	Pancrea
3	chr12:122028600-122048000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:122028600-122048400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:122028800-122048400	Weak transcription	Brain Angular Gyrus	brain
6	chr12:122028800-122049000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:122028800-122064000	Weak transcription	Right Atrium	heart
8	chr12:122029200-122038000	Weak transcription	NHLF	lung
9	chr12:122029200-122038200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:122029200-122038800	Weak transcription	Brain Hippocampus Middle	brain
11	chr12:122029200-122038800	Weak transcription	HSMMtube	muscle
12	chr12:122029200-122049800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:122030200-122037200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:122030600-122039000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:122030800-122037200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:122031200-122038600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr12:122033200-122049600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:122033400-122041600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:122033800-122049600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:122034000-122037800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:122034000-122046400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:122034000-122048400	Weak transcription	Brain Anterior Caudate	brain
23	chr12:122034400-122038000	Weak transcription	Dnd41	blood
24	chr12:122034600-122037800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:122034600-122048400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:122034800-122040400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:122035000-122048000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:122035000-122048200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr12:122035800-122039200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:122036000-122037800	Enhancers	Fetal Intestine Large	intestine
31	chr12:122036000-122041000	Enhancers	Fetal Intestine Small	intestine
32	chr12:122036200-122037200	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr12:122036200-122037200	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr12:122036200-122038000	Enhancers	HepG2	liver
35	chr12:122036400-122037200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:122036400-122037400	Enhancers	A549	lung
37	chr12:122036400-122037400	Enhancers	K562	blood
38	chr12:122036400-122039800	Enhancers	Stomach Mucosa	stomach
39	chr12:122036400-122048000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr12:122036600-122037200	Enhancers	Primary T cells from cord blood	blood
41	chr12:122036600-122037200	Enhancers	Gastric	stomach
42	chr12:122036600-122038200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:122036600-122040400	Weak transcription	Colonic Mucosa	Colon
44	chr12:122036800-122037200	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr12:122037000-122037200	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr12:122037000-122037200	Enhancers	Stomach Smooth Muscle	stomach
47	chr12:122037000-122038600	Weak transcription	Rectal Mucosa Donor 29	rectum

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