Variant report

Variant	rs2942368
Chromosome Location	chr12:122116794-122116795
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122110522..122113228-chr12:122115462..122118527,3	MCF-7	breast:
2	chr12:122111338..122114231-chr12:122116440..122119005,2	K562	blood:
3	chr12:122115091..122119007-chr12:122123231..122126528,5	K562	blood:

Variant related genes	Relation type
ENSG00000139714	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10743188	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10840652	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11043179	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12320939	0.94[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1877484	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2137434	0.80[MEX][hapmap]
rs2309142	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2458404	0.89[GIH][hapmap]
rs2466145	0.80[MEX][hapmap]
rs2669163	0.96[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2669165	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2669166	1.00[ASW][hapmap];0.85[CEU][hapmap];0.98[GIH][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2669168	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2720021	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2720022	1.00[ASW][hapmap];0.96[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2720024	0.83[AMR][1000 genomes]
rs2720025	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2720035	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2720041	0.88[MEX][hapmap];0.81[TSI][hapmap]
rs2942370	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2942379	1.00[ASW][hapmap];0.85[CEU][hapmap];0.98[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2954116	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3825175	0.94[ASW][hapmap];0.88[CEU][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3934658	0.88[ASW][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap]
rs6486789	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7135617	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs7297028	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7397295	0.85[AFR][1000 genomes]
rs7399127	0.88[ASW][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap]
rs7967415	0.80[MEX][hapmap]
rs7978609	0.86[EUR][1000 genomes]
rs7978866	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs925531	0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv1040169	chr12:122096825-122209555	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv527988	chr12:122114593-122116794	Weak transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2942368	GTF2H3	cis	cerebellum	SCAN
rs2942368	LRRC43	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122111400-122116800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:122111400-122116800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:122111400-122116800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:122111400-122116800	Weak transcription	Fetal Thymus	thymus
5	chr12:122111400-122117000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:122111400-122117000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:122111400-122117000	Weak transcription	Thymus	Thymus
8	chr12:122111400-122124200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:122111400-122124400	Weak transcription	Brain Anterior Caudate	brain
10	chr12:122111400-122124800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:122111600-122116800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:122111600-122116800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:122111600-122116800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr12:122111600-122117000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:122111600-122117000	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:122111600-122119800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:122111600-122124600	Weak transcription	Fetal Kidney	kidney
18	chr12:122111800-122117200	Weak transcription	Brain Substantia Nigra	brain
19	chr12:122113000-122117000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:122114600-122117000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:122116000-122116800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:122116000-122117000	Enhancers	K562	blood
23	chr12:122116000-122117600	Enhancers	Fetal Muscle Leg	muscle
24	chr12:122116200-122117000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:122116200-122117200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:122116200-122117400	Enhancers	Fetal Muscle Trunk	muscle
27	chr12:122116200-122118000	Enhancers	Brain Germinal Matrix	brain
28	chr12:122116400-122117200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:122116400-122117200	Enhancers	HSMM	muscle
30	chr12:122116400-122117400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:122116400-122117400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:122116600-122117000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:122116600-122117400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr12:122116600-122117600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:122116600-122118600	Enhancers	Placenta	Placenta

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