Variant report

Variant	rs11611002
Chromosome Location	chr12:21626152-21626153
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1024734	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11046044	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11835956	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12422251	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12423381	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12818516	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12826040	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1860948	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2417987	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4539382	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4762826	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6487224	1.00[CEU][hapmap]
rs7131809	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7133131	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7133853	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7138089	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7298136	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7310391	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7314131	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs738027	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7957415	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7959893	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7971245	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7973116	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7974260	1.00[CEU][hapmap]
rs7974817	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9668302	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]

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	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription 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	46 gene(s)	inside rSNPs	diseases
3	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1054220	chr12:21612158-21692103	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv3433505	chr12:21626096-21626380	Strong transcription Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11611002	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs11611002	PYROXD1	cis	Esophagus Muscularis	GTEx
rs11611002	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs11611002	FLJ22028	cis	normal skin	skin_eQTL
rs11611002	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs11611002	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21592000-21631000	Weak transcription	Psoas Muscle	Psoas
2	chr12:21592800-21631400	Weak transcription	K562	blood
3	chr12:21595600-21626200	Weak transcription	Right Ventricle	heart
4	chr12:21595800-21631400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:21595800-21632600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:21595800-21633200	Weak transcription	Gastric	stomach
7	chr12:21595800-21650000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:21596000-21631600	Weak transcription	Pancreas	Pancrea
9	chr12:21597400-21636000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:21599000-21629600	Weak transcription	Stomach Mucosa	stomach
11	chr12:21607000-21645800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:21610600-21626200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:21611000-21652800	Weak transcription	Small Intestine	intestine
14	chr12:21611000-21653600	Weak transcription	Esophagus	oesophagus
15	chr12:21611200-21631400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:21611200-21640800	Weak transcription	Fetal Heart	heart
17	chr12:21611800-21626600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:21612200-21630800	Weak transcription	Spleen	Spleen
19	chr12:21612400-21627200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:21612600-21631000	Weak transcription	Lung	lung
21	chr12:21613800-21631600	Weak transcription	Fetal Stomach	stomach
22	chr12:21614800-21652800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:21616600-21631800	Weak transcription	Fetal Intestine Small	intestine
24	chr12:21617000-21653000	Weak transcription	Colonic Mucosa	Colon
25	chr12:21617400-21630800	Weak transcription	Thymus	Thymus
26	chr12:21617600-21626800	Weak transcription	Fetal Lung	lung
27	chr12:21617800-21626200	Weak transcription	Brain Substantia Nigra	brain
28	chr12:21619400-21627000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr12:21619800-21638400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:21619800-21652200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr12:21619800-21652400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:21619800-21652400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr12:21620000-21630000	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr12:21620200-21652600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:21620400-21629800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:21620400-21637800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr12:21620600-21636600	Strong transcription	Dnd41	blood
38	chr12:21620600-21652200	Strong transcription	Primary B cells from peripheral blood	blood
39	chr12:21620800-21636600	Strong transcription	Fetal Thymus	thymus
40	chr12:21621000-21630600	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:21621600-21626200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:21623000-21635400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:21623200-21649400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr12:21623400-21633400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr12:21623800-21627000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:21623800-21629600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:21623800-21629800	Strong transcription	NH-A	brain
48	chr12:21623800-21630000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:21623800-21636600	Strong transcription	Liver	Liver
50	chr12:21623800-21636800	Strong transcription	Primary T helper cells PMA-I stimulated	--

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