Variant report

Variant	rs7961112
Chromosome Location	chr12:50513519-50513520
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50506976..50509315-chr12:50512886..50514757,3	K562	blood:
2	chr12:50510353..50512301-chr12:50513057..50515415,2	K562	blood:
3	chr12:50513121..50517277-chr12:50517671..50521204,4	MCF-7	breast:
4	chr12:50512025..50513776-chr12:50559393..50561969,2	MCF-7	breast:
5	chr12:50513117..50516095-chr12:50518308..50520675,3	K562	blood:
6	chr12:50504895..50507498-chr12:50512482..50515401,3	MCF-7	breast:
7	chr12:50506326..50509315-chr12:50512899..50514726,2	K562	blood:
8	chr12:50510457..50512619-chr12:50512712..50515354,2	MCF-7	breast:
9	chr12:50512748..50515503-chr12:50523146..50524991,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272368	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000139624	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	0.95[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];0.90[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];0.93[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	0.93[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];0.95[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	0.81[AFR][1000 genomes];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];0.93[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	0.99[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]
rs7294618	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]
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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307469	1.00[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]
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
rs7961112	ATF1	cis	parietal	SCAN
rs7961112	LASS5	cis	parietal	SCAN
rs7961112	CERS5	cis	Muscle Skeletal	GTEx
rs7961112	CERS5	cis	Nerve Tibial	GTEx
rs7961112	LASS5	cis	cerebellum	SCAN
rs7961112	SNORA2A	cis	parietal	SCAN
rs7961112	DIP2B	Cis_1M	lymphoblastoid	RTeQTL

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	chr12:50507000-50513600	Weak transcription	Fetal Kidney	kidney
4	chr12:50507000-50513800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:50507000-50520800	Weak transcription	Fetal Lung	lung
6	chr12:50507000-50520800	Weak transcription	NH-A	brain
7	chr12:50507000-50522400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr12:50507000-50522800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:50507000-50522800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:50507000-50523600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:50507000-50537400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:50507000-50539600	Weak transcription	Stomach Mucosa	stomach
13	chr12:50507200-50513800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:50507200-50515400	Weak transcription	Fetal Brain Male	brain
15	chr12:50507200-50519000	Weak transcription	HUVEC	blood vessel
16	chr12:50507200-50520800	Weak transcription	NHDF-Ad	bronchial
17	chr12:50507200-50520800	Weak transcription	NHLF	lung
18	chr12:50507200-50521400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr12:50507200-50522600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:50507200-50523600	Weak transcription	Right Atrium	heart
21	chr12:50507200-50532000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr12:50507400-50514600	Genic enhancers	Primary T cells fromperipheralblood	blood
23	chr12:50508400-50513800	Weak transcription	Colonic Mucosa	Colon
24	chr12:50508400-50518200	Strong transcription	Fetal Stomach	stomach
25	chr12:50508600-50518200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:50508600-50518200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:50508800-50518000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:50509200-50518200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:50509200-50518400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:50509400-50518000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:50509400-50518200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:50509400-50518400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:50509400-50519600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:50509400-50521600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr12:50509400-50522600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr12:50509800-50513800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:50510000-50517800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:50510000-50518200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:50510400-50515200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:50510800-50513600	Weak transcription	HSMM	muscle
41	chr12:50510800-50513600	Weak transcription	HSMMtube	muscle
42	chr12:50510800-50523800	Weak transcription	Psoas Muscle	Psoas
43	chr12:50510800-50528400	Strong transcription	Liver	Liver
44	chr12:50511200-50514000	Weak transcription	Fetal Brain Female	brain
45	chr12:50511200-50519000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr12:50511200-50538200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:50511400-50518000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr12:50511400-50518200	Strong transcription	Lung	lung
49	chr12:50511400-50538600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:50511600-50513800	Weak transcription	Small Intestine	intestine

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