Variant report

Variant	rs7297421
Chromosome Location	chr12:50518926-50518927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50504999..50508637-chr12:50517322..50519426,3	K562	blood:
2	chr12:50496011..50498479-chr12:50517692..50519863,2	MCF-7	breast:
3	chr12:50513121..50517277-chr12:50517671..50521204,4	MCF-7	breast:
4	chr12:50513117..50516095-chr12:50518308..50520675,3	K562	blood:

Variant related genes	Relation type
ENSG00000272368	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000167588	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1044370	0.90[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap]
rs10747570	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169294	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11831413	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12815871	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12824125	0.86[EUR][1000 genomes]
rs12830386	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1862043	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2178173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2358538	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs34573394	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35549836	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35998534	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4459386	0.89[ASW][hapmap];0.89[YRI][hapmap]
rs56709084	0.86[ASN][1000 genomes]
rs646782	1.00[CHB][hapmap]
rs6580729	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66768395	0.81[ASN][1000 genomes]
rs706791	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs706792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs706793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7136570	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];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7279	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];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294548	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7301649	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7301740	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302981	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];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7308356	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7532	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957659	0.89[ASW][hapmap];0.85[LWK][hapmap];0.89[YRI][hapmap]
rs7967705	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7967844	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7972842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836170	0.86[ASN][1000 genomes]
rs836171	0.88[ASN][1000 genomes]
rs836172	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs836173	0.84[ASN][1000 genomes]
rs836174	0.84[ASN][1000 genomes]
rs836176	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs836177	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs836179	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs836180	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs836181	0.80[ASN][1000 genomes]
rs844347	0.84[GIH][hapmap]
rs860698	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7297421	SNORA2A	cis	parietal	SCAN
rs7297421	LASS5	cis	parietal	SCAN
rs7297421	KRT84	cis	cerebellum	SCAN
rs7297421	MCRS1	cis	parietal	SCAN
rs7297421	CERS5	cis	Nerve Tibial	GTEx
rs7297421	LASS5	cis	cerebellum	SCAN
rs7297421	DIP2B	cis	cerebellum	SCAN
rs7297421	LASS5	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50506800-50521000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:50506800-50523600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:50507000-50520800	Weak transcription	Fetal Lung	lung
4	chr12:50507000-50520800	Weak transcription	NH-A	brain
5	chr12:50507000-50522400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:50507000-50522800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:50507000-50522800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:50507000-50523600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:50507000-50537400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:50507000-50539600	Weak transcription	Stomach Mucosa	stomach
11	chr12:50507200-50519000	Weak transcription	HUVEC	blood vessel
12	chr12:50507200-50520800	Weak transcription	NHDF-Ad	bronchial
13	chr12:50507200-50520800	Weak transcription	NHLF	lung
14	chr12:50507200-50521400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:50507200-50522600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:50507200-50523600	Weak transcription	Right Atrium	heart
17	chr12:50507200-50532000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:50509400-50519600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:50509400-50521600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr12:50509400-50522600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr12:50510800-50523800	Weak transcription	Psoas Muscle	Psoas
22	chr12:50510800-50528400	Strong transcription	Liver	Liver
23	chr12:50511200-50519000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr12:50511200-50538200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:50511400-50538600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:50512200-50519400	Weak transcription	Fetal Heart	heart
27	chr12:50512600-50519000	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr12:50512600-50519200	Strong transcription	Adipose Nuclei	Adipose
29	chr12:50512600-50522800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:50512600-50529200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:50512600-50538200	Strong transcription	Primary B cells from cord blood	blood
32	chr12:50513000-50519000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr12:50513000-50519000	Strong transcription	Fetal Thymus	thymus
34	chr12:50513000-50522200	Strong transcription	Stomach Smooth Muscle	stomach
35	chr12:50513200-50521200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:50513600-50520600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:50514000-50519000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:50514200-50522800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr12:50514400-50520000	Strong transcription	Brain Hippocampus Middle	brain
40	chr12:50514400-50520800	Weak transcription	Fetal Kidney	kidney
41	chr12:50514400-50520800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr12:50514600-50519000	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr12:50514800-50520600	Weak transcription	Osteobl	bone
44	chr12:50514800-50523600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr12:50515000-50520600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr12:50515000-50520600	Weak transcription	HMEC	breast
47	chr12:50515000-50521200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr12:50515200-50519000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr12:50515200-50520600	Weak transcription	Colonic Mucosa	Colon
50	chr12:50515400-50520600	Weak transcription	Aorta	Aorta

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