Variant report

Variant	rs12286317
Chromosome Location	chr11:77389020-77389021
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10899394	0.81[GIH][hapmap];0.88[TSI][hapmap]
rs10899399	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899404	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11237244	0.82[TSI][hapmap]
rs11237263	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237280	0.85[EUR][1000 genomes]
rs11237318	0.85[ASN][1000 genomes]
rs11603438	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11604207	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12285765	0.91[ASN][1000 genomes]
rs17752006	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783544	0.91[ASN][1000 genomes]
rs2032395	0.84[GIH][hapmap];0.82[TSI][hapmap]
rs2154972	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs24356	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs2508189	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34130561	0.82[EUR][1000 genomes]
rs4322421	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4344516	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs484363	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4945220	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs537811	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56218634	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs588217	0.90[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.91[ASN][1000 genomes]
rs598071	0.91[ASN][1000 genomes]
rs614495	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs621456	1.00[CHB][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs623173	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs623907	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs628668	0.90[JPT][hapmap]
rs635195	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs636971	0.91[ASN][1000 genomes]
rs643388	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs648601	0.90[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.91[ASN][1000 genomes]
rs650171	0.90[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs663674	0.87[ASN][1000 genomes]
rs667225	0.91[ASN][1000 genomes]
rs668701	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap]
rs670090	0.85[ASN][1000 genomes]
rs684813	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs694845	0.91[ASN][1000 genomes]
rs695046	0.87[ASN][1000 genomes]
rs7122968	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7123080	0.94[CEU][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7129556	0.80[GIH][hapmap]
rs72945592	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72945598	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72947625	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72947668	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72949616	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72949618	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7950873	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7951033	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs947841	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1038974	chr11:77284036-77431228	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1041384	chr11:77284558-77419809	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1048892	chr11:77290458-77431228	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
6	nsv1053074	chr11:77290458-77435831	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv468641	chr11:77301341-77420314	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv555452	chr11:77301341-77420314	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1035494	chr11:77309696-77431228	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12286317	AQP11	cis	parietal	SCAN
rs12286317	C11orf67	cis	cerebellum	SCAN
rs12286317	INTS4	cis	cerebellum	SCAN
rs12286317	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77360400-77419200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:77370000-77410400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:77373800-77413600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:77374000-77416200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:77374200-77417400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr11:77374800-77414000	Strong transcription	Fetal Thymus	thymus
7	chr11:77375000-77390200	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:77375000-77411200	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr11:77375000-77411200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr11:77375000-77413000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr11:77375200-77411000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr11:77375200-77411000	Strong transcription	Liver	Liver
13	chr11:77375200-77413600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:77375400-77389800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr11:77375400-77389800	Strong transcription	Placenta	Placenta
16	chr11:77375400-77390000	Strong transcription	Adipose Nuclei	Adipose
17	chr11:77375400-77391200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:77375400-77394600	Strong transcription	Fetal Muscle Leg	muscle
19	chr11:77375400-77395400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:77375400-77396400	Strong transcription	Primary hematopoietic stem cells	blood
21	chr11:77375400-77404800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr11:77375400-77411000	Strong transcription	Dnd41	blood
23	chr11:77375600-77390200	Strong transcription	Primary B cells from cord blood	blood
24	chr11:77375600-77395200	Strong transcription	Primary T cells from cord blood	blood
25	chr11:77375600-77395800	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:77375600-77405000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr11:77375600-77411200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr11:77375600-77413200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr11:77375600-77413400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:77375800-77404800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:77376200-77394800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr11:77376800-77415600	Strong transcription	Primary B cells from peripheral blood	blood
33	chr11:77377600-77391800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr11:77377600-77410400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr11:77377800-77389200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr11:77377800-77389200	Strong transcription	Fetal Lung	lung
37	chr11:77377800-77390000	Strong transcription	Colon Smooth Muscle	Colon
38	chr11:77377800-77395200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr11:77377800-77395200	Strong transcription	Fetal Muscle Trunk	muscle
40	chr11:77378000-77389200	Strong transcription	Fetal Brain Female	brain
41	chr11:77378000-77389400	Strong transcription	Brain Hippocampus Middle	brain
42	chr11:77378000-77395600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr11:77378000-77397800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr11:77378600-77393800	Weak transcription	Gastric	stomach
45	chr11:77379600-77391000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr11:77380000-77389200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr11:77380400-77392800	Weak transcription	Fetal Heart	heart
48	chr11:77380600-77390000	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:77381400-77393600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:77381400-77403000	Weak transcription	Aorta	Aorta

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