Variant report

Variant	rs12033829
Chromosome Location	chr1:247048378-247048379
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10436931	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10924862	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10924863	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10924866	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[LWK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs10924867	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs10924868	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10924869	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11585265	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12023594	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12029050	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12032354	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12033144	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12691532	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12728361	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12739487	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12739603	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12748665	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12752855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1892116	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2067916	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35716055	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6426191	0.90[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs7551797	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	esv1810844	chr1:246988018-247054824	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv5276	chr1:247028364-247073098	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
10	nsv1000602	chr1:247044627-247226568	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12033829	NLRP3	cis	cerebellum	SCAN
rs12033829	AHCTF1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247002200-247082400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr1:247002400-247081000	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr1:247004000-247053600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:247004200-247083400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:247005200-247079800	Weak transcription	Stomach Mucosa	stomach
6	chr1:247006600-247071600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:247018400-247056400	Weak transcription	Fetal Heart	heart
8	chr1:247020400-247072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:247024200-247052000	Weak transcription	Pancreas	Pancrea
10	chr1:247025200-247052000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:247031600-247071400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:247032800-247051600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:247033200-247060800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:247033600-247058000	Weak transcription	Colonic Mucosa	Colon
15	chr1:247033800-247051600	Weak transcription	HSMMtube	muscle
16	chr1:247033800-247070800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:247035000-247051600	Weak transcription	Psoas Muscle	Psoas
18	chr1:247035800-247051600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:247036200-247052000	Weak transcription	Small Intestine	intestine
20	chr1:247037200-247051800	Weak transcription	Brain Germinal Matrix	brain
21	chr1:247037400-247052000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:247038000-247050200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:247039000-247049000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:247039000-247051600	Weak transcription	Spleen	Spleen
25	chr1:247039000-247057200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:247039000-247070400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:247039200-247050000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:247039200-247051600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:247039200-247051600	Weak transcription	Lung	lung
30	chr1:247039200-247052000	Weak transcription	Fetal Brain Male	brain
31	chr1:247039200-247052000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:247039400-247051400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:247039400-247052000	Weak transcription	Esophagus	oesophagus
34	chr1:247039800-247051400	Weak transcription	Right Ventricle	heart
35	chr1:247040200-247050600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:247040200-247050800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:247040400-247051400	Weak transcription	Brain Angular Gyrus	brain
38	chr1:247040400-247051400	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:247040400-247051600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:247040400-247051600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:247040400-247065000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr1:247040600-247049800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:247040600-247051600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:247040600-247052200	Weak transcription	Brain Substantia Nigra	brain
45	chr1:247041000-247048400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:247041200-247050000	Weak transcription	NHLF	lung
47	chr1:247041200-247051600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:247042200-247048600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:247042400-247048400	Weak transcription	NHEK	skin
50	chr1:247043200-247049000	Weak transcription	Fetal Muscle Leg	muscle

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