Variant report

Variant	rs12631824
Chromosome Location	chr3:121398425-121398426
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs12489511	1.00[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs12490565	0.95[CEU][hapmap];0.92[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs13067629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1492177	0.95[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs1574655	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1574735	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17849995	0.80[EUR][1000 genomes]
rs1873645	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1919552	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1919557	0.87[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];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1986351	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1986874	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2001390	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2001391	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070179	0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2332056	0.95[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap]
rs2840143	0.95[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs35295338	0.87[EUR][1000 genomes]
rs3772127	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4478028	0.83[EUR][1000 genomes]
rs4676684	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4676685	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4676686	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4676751	0.81[EUR][1000 genomes]
rs59740137	0.80[EUR][1000 genomes]
rs6438645	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6438660	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs6770719	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs6776703	0.81[EUR][1000 genomes]
rs6791896	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792659	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6794341	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6794677	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6802033	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6803839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807711	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7375038	0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7429247	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7430165	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611913	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7620842	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7646346	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs7646585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289172	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9289173	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9681209	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9809114	0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9812411	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9829053	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9832267	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9835182	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9854052	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9861992	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9864907	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876021	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12631824	HCLS1	cis	lymphoblastoid	seeQTL
rs12631824	SLC15A2	cis	parietal	SCAN
rs12631824	MUC13	cis	cerebellum	SCAN
rs12631824	PTPLB	cis	cerebellum	SCAN
rs12631824	ADPRH	cis	parietal	SCAN
rs12631824	SLC15A2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121379400-121402400	Strong transcription	Fetal Intestine Large	intestine
2	chr3:121380000-121402600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:121380400-121402400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:121380400-121402800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:121380400-121406600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:121380600-121413800	Weak transcription	Stomach Mucosa	stomach
7	chr3:121381000-121401800	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:121381000-121403200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:121381400-121406800	Strong transcription	Duodenum Mucosa	Duodenum
10	chr3:121381600-121401600	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr3:121381600-121402200	Strong transcription	Placenta	Placenta
12	chr3:121381600-121402400	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr3:121381600-121402400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:121381600-121402600	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr3:121381600-121402800	Strong transcription	Liver	Liver
16	chr3:121381800-121401200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:121381800-121402600	Strong transcription	Primary T cells from cord blood	blood
18	chr3:121382000-121401800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:121382200-121401600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:121382400-121401800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:121382600-121399400	Strong transcription	Left Ventricle	heart
22	chr3:121382600-121401600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:121382800-121402600	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:121383000-121400200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:121384200-121399200	Strong transcription	Fetal Muscle Leg	muscle
26	chr3:121384200-121402600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:121386600-121447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr3:121390200-121402000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr3:121390200-121402400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr3:121390400-121402400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:121390800-121403400	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:121391200-121400200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:121391400-121400200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr3:121391800-121402600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr3:121392400-121399000	Strong transcription	Lung	lung
36	chr3:121392400-121401200	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:121392800-121401400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:121392800-121401600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:121392800-121401600	Strong transcription	Primary B cells from cord blood	blood
40	chr3:121392800-121401800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr3:121393000-121401800	Strong transcription	HSMM	muscle
42	chr3:121393400-121401800	Strong transcription	GM12878-XiMat	blood
43	chr3:121394200-121399600	Strong transcription	Hela-S3	cervix
44	chr3:121394200-121400800	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:121394600-121402200	Strong transcription	HSMMtube	muscle
46	chr3:121395600-121398800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:121396000-121398600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:121396000-121398600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:121396000-121398600	Weak transcription	Fetal Brain Male	brain
50	chr3:121396000-121398600	Weak transcription	Small Intestine	intestine

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