Variant report

Variant	rs4997380
Chromosome Location	chr12:122838956-122838957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10161534	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10734915	0.91[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10734918	0.82[EUR][1000 genomes]
rs10734924	0.88[JPT][hapmap];0.80[TSI][hapmap]
rs10744208	0.81[EUR][1000 genomes]
rs10744209	0.81[EUR][1000 genomes]
rs10744210	0.82[EUR][1000 genomes]
rs10744211	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs10773075	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10773088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10773103	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10773104	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10773152	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs10773167	0.82[EUR][1000 genomes]
rs10773208	0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs10846664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10846688	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10846699	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10846746	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10846764	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10846792	0.84[EUR][1000 genomes]
rs10846830	0.82[EUR][1000 genomes]
rs10846921	0.94[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs10846978	0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs10998	0.87[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs11057786	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11057797	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11057882	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11058034	0.82[EUR][1000 genomes]
rs11058226	0.94[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs11058402	0.88[JPT][hapmap]
rs11616082	0.82[EUR][1000 genomes]
rs11836188	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12369858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs12372756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12581249	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1473553	0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap]
rs1553179	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1803290	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1818050	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1973463	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2062488	0.89[CEU][hapmap];0.86[TSI][hapmap]
rs2173582	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2341439	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28730465	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34129612	0.82[EUR][1000 genomes]
rs3817011	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4039670	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4758643	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4758648	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs4758662	0.82[EUR][1000 genomes]
rs4758666	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs4758667	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55834409	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6488933	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6488939	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6488951	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6488958	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6489002	0.82[EUR][1000 genomes]
rs7135419	0.82[EUR][1000 genomes]
rs7294559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7301515	0.84[CEU][hapmap];0.91[TSI][hapmap]
rs7314638	0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs7397299	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7952868	0.88[EUR][1000 genomes]
rs7953007	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7956480	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7964138	0.89[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs7969429	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7973869	0.81[EUR][1000 genomes]
rs7974262	0.82[EUR][1000 genomes]
rs7975747	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9988963	0.87[CHD][hapmap];0.88[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4997380	NME2P1	cis	cerebellum	SCAN
rs4997380	RNF34	cis	parietal	SCAN
rs4997380	GTF2H3	cis	cerebellum	SCAN
rs4997380	B3GNT4	cis	cerebellum	SCAN
rs4997380	GATC	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122791200-122841600	Strong transcription	Placenta	Placenta
2	chr12:122804200-122839000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr12:122812800-122839400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:122812800-122839400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:122812800-122844000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:122812800-122850600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:122813000-122839400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr12:122818400-122852800	Weak transcription	Stomach Mucosa	stomach
9	chr12:122818600-122844200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:122819600-122839200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:122820200-122839400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:122823000-122840200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:122823200-122839400	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:122825800-122839200	Weak transcription	Fetal Kidney	kidney
15	chr12:122828800-122841200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr12:122830400-122841200	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr12:122830600-122839600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:122830600-122840600	Strong transcription	HSMMtube	muscle
19	chr12:122830600-122840800	Strong transcription	A549	lung
20	chr12:122830600-122841000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:122830600-122841200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:122830600-122841200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr12:122830600-122841200	Strong transcription	Brain Germinal Matrix	brain
24	chr12:122830800-122839600	Strong transcription	Fetal Muscle Trunk	muscle
25	chr12:122830800-122840400	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr12:122830800-122841200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr12:122830800-122841800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:122830800-122842400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:122831000-122841000	Strong transcription	Fetal Stomach	stomach
30	chr12:122831200-122840600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:122831200-122840800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr12:122831600-122839000	Weak transcription	Brain Substantia Nigra	brain
33	chr12:122832600-122840600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:122833400-122841200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:122833600-122840600	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:122833800-122840600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:122833800-122841200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:122834000-122840200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:122834200-122840400	Weak transcription	K562	blood
40	chr12:122834400-122841200	Strong transcription	Hela-S3	cervix
41	chr12:122834400-122845400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr12:122834600-122839800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:122834600-122840000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:122834600-122840000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr12:122834800-122839600	Strong transcription	Primary B cells from peripheral blood	blood
46	chr12:122834800-122841000	Strong transcription	Primary B cells from cord blood	blood
47	chr12:122835000-122840600	Strong transcription	NHEK	skin
48	chr12:122835200-122839000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr12:122835200-122839800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr12:122835400-122841400	Strong transcription	Dnd41	blood

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