Variant report

Variant	rs7294618
Chromosome Location	chr12:50512975-50512976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50506976..50509315-chr12:50512886..50514757,3	K562	blood:
2	chr12:50512025..50513776-chr12:50559393..50561969,2	MCF-7	breast:
3	chr12:50504895..50507498-chr12:50512482..50515401,3	MCF-7	breast:
4	chr12:50506326..50509315-chr12:50512899..50514726,2	K562	blood:
5	chr12:50510457..50512619-chr12:50512712..50515354,2	MCF-7	breast:
6	chr12:50512748..50515503-chr12:50523146..50524991,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139624	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000272368	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10735824	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783338	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169270	0.80[GIH][hapmap]
rs11169278	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12369049	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369104	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12819883	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1554844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554845	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17124432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17124514	0.88[JPT][hapmap]
rs2204683	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3184122	0.84[CEU][hapmap]
rs34167640	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741562	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs376184	0.84[GIH][hapmap]
rs4898546	0.84[GIH][hapmap]
rs59262224	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580728	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66782120	0.85[ASN][1000 genomes]
rs706794	0.85[GIH][hapmap]
rs7135322	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7138420	0.83[ASW][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap]
rs7138622	0.87[YRI][hapmap]
rs7138945	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7307230	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307469	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315690	0.88[ASW][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap]
rs7398567	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7961065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961112	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964698	0.89[EUR][1000 genomes]
rs7967979	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968119	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7972465	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7978904	0.83[EUR][1000 genomes]
rs836178	0.85[GIH][hapmap]
rs9364	0.88[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7294618	LASS5	cis	cerebellum	SCAN
rs7294618	ATF1	cis	parietal	SCAN
rs7294618	LASS5	cis	parietal	SCAN
rs7294618	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs7294618	CERS5	cis	Nerve Tibial	GTEx
rs7294618	CERS5	cis	Muscle Skeletal	GTEx
rs7294618	SNORA2A	cis	parietal	SCAN

Chromatin state (count:123 , 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	chr12:50507000-50513000	Weak transcription	Esophagus	oesophagus
4	chr12:50507000-50513200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:50507000-50513200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:50507000-50513600	Weak transcription	Fetal Kidney	kidney
7	chr12:50507000-50513800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:50507000-50520800	Weak transcription	Fetal Lung	lung
9	chr12:50507000-50520800	Weak transcription	NH-A	brain
10	chr12:50507000-50522400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:50507000-50522800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr12:50507000-50522800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:50507000-50523600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:50507000-50537400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr12:50507000-50539600	Weak transcription	Stomach Mucosa	stomach
16	chr12:50507200-50513000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:50507200-50513000	Weak transcription	Osteobl	bone
18	chr12:50507200-50513200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:50507200-50513200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:50507200-50513800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:50507200-50515400	Weak transcription	Fetal Brain Male	brain
22	chr12:50507200-50519000	Weak transcription	HUVEC	blood vessel
23	chr12:50507200-50520800	Weak transcription	NHDF-Ad	bronchial
24	chr12:50507200-50520800	Weak transcription	NHLF	lung
25	chr12:50507200-50521400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:50507200-50522600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:50507200-50523600	Weak transcription	Right Atrium	heart
28	chr12:50507200-50532000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr12:50507400-50513200	Weak transcription	Brain Anterior Caudate	brain
30	chr12:50507400-50514600	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr12:50508000-50513200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr12:50508000-50513200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr12:50508000-50513200	Weak transcription	Aorta	Aorta
34	chr12:50508400-50513000	Weak transcription	HepG2	liver
35	chr12:50508400-50513400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:50508400-50513800	Weak transcription	Colonic Mucosa	Colon
37	chr12:50508400-50518200	Strong transcription	Fetal Stomach	stomach
38	chr12:50508600-50513400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr12:50508600-50518200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:50508600-50518200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr12:50508800-50518000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:50509200-50518200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:50509200-50518400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:50509400-50518000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:50509400-50518200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:50509400-50518400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:50509400-50519600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:50509400-50521600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr12:50509400-50522600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr12:50509800-50513800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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