Variant report

Variant	rs12285441
Chromosome Location	chr11:86785810-86785811
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1026410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898592	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10898598	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11234927	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11234931	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11234934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11234935	1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11234936	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11234949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11234974	0.81[ASN][1000 genomes]
rs11234975	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.81[ASN][1000 genomes]
rs11234979	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs11234981	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11234987	0.81[ASN][1000 genomes]
rs11821269	0.81[ASN][1000 genomes]
rs11821284	0.81[ASN][1000 genomes]
rs11824728	0.81[ASN][1000 genomes]
rs11825950	0.81[ASN][1000 genomes]
rs12270428	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12271109	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12273408	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12273779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12274647	0.81[AMR][1000 genomes]
rs12279443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12282651	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12282966	0.81[ASN][1000 genomes]
rs12283115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12283210	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12286127	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12286867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12288001	0.81[ASN][1000 genomes]
rs12289216	1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12289267	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12289978	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13377595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17758940	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17759040	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17820908	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2156765	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2220472	0.81[ASN][1000 genomes]
rs28822396	0.81[ASN][1000 genomes]
rs35036190	0.81[ASN][1000 genomes]
rs3740660	1.00[CEU][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap]
rs4315108	0.81[ASN][1000 genomes]
rs4578415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4594023	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473996	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs475752	0.89[ASW][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs477156	1.00[CHB][hapmap]
rs482450	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs502191	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs502427	1.00[JPT][hapmap]
rs504084	0.89[ASW][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs509485	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs513938	1.00[JPT][hapmap]
rs515560	1.00[JPT][hapmap]
rs515623	1.00[JPT][hapmap]
rs529147	1.00[JPT][hapmap]
rs532442	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs533416	1.00[JPT][hapmap]
rs554757	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55790509	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56028118	0.81[AMR][1000 genomes]
rs560392	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs561463	1.00[JPT][hapmap]
rs56880471	0.81[ASN][1000 genomes]
rs570898	1.00[JPT][hapmap]
rs574378	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs574417	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs575496	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs576532	1.00[CHB][hapmap]
rs57664476	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57933396	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs581079	0.80[GIH][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap]
rs58190299	0.81[ASN][1000 genomes]
rs588499	1.00[JPT][hapmap]
rs589193	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap]
rs591818	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs605456	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs60711353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61904170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61904173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61904180	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61904191	0.81[ASN][1000 genomes]
rs61904209	0.81[ASN][1000 genomes]
rs61904213	0.81[ASN][1000 genomes]
rs61904215	0.81[ASN][1000 genomes]
rs61906173	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61906192	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61906193	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61906194	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61906203	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61906207	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs620313	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs621758	1.00[JPT][hapmap]
rs624256	1.00[JPT][hapmap]
rs631756	1.00[JPT][hapmap]
rs633629	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs638848	0.89[ASW][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs653419	0.89[ASW][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap]
rs654083	0.89[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs654152	1.00[JPT][hapmap]
rs654451	1.00[JPT][hapmap]
rs655951	1.00[JPT][hapmap]
rs668448	1.00[JPT][hapmap]
rs676503	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs679690	1.00[JPT][hapmap]
rs681642	1.00[JPT][hapmap]
rs7115725	0.81[ASN][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	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1037042	chr11:86586876-86978492	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
4	nsv541119	chr11:86586876-86978492	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv898058	chr11:86754948-86889284	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv898059	chr11:86754948-86949369	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1043562	chr11:86755535-87547185	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv541120	chr11:86755535-87547185	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv1046288	chr11:86757573-87158571	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	esv1844274	chr11:86776992-86872908	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12285441	ME3	cis	cerebellum	SCAN
rs12285441	C11orf82	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86750800-86787400	Weak transcription	A549	lung
2	chr11:86751000-86786800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:86751000-86787400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:86751400-86786400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr11:86751600-86787000	Weak transcription	Aorta	Aorta
6	chr11:86758200-86786400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:86769000-86786400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:86769200-86786400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr11:86769200-86786800	Weak transcription	Brain Anterior Caudate	brain
10	chr11:86769200-86791200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr11:86769200-86792400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:86769600-86786600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:86770400-86808200	Weak transcription	HUVEC	blood vessel
14	chr11:86771000-86786600	Weak transcription	Fetal Brain Male	brain
15	chr11:86771200-86786800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr11:86771800-86786000	Weak transcription	Fetal Lung	lung
17	chr11:86773000-86790800	Weak transcription	NHLF	lung
18	chr11:86773000-86792000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr11:86774600-86792400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr11:86774800-86786400	Weak transcription	Lung	lung
21	chr11:86774800-86786800	Weak transcription	Pancreas	Pancrea
22	chr11:86774800-86786800	Weak transcription	Right Ventricle	heart
23	chr11:86774800-86787600	Weak transcription	NHEK	skin
24	chr11:86774800-86806400	Weak transcription	Small Intestine	intestine
25	chr11:86775000-86786600	Weak transcription	Colon Smooth Muscle	Colon
26	chr11:86775600-86786400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:86775600-86791400	Weak transcription	HSMM	muscle
28	chr11:86776200-86787000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr11:86776400-86786000	Weak transcription	Fetal Thymus	thymus
30	chr11:86776400-86792400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:86776600-86786600	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:86776600-86793000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr11:86776600-86815600	Weak transcription	HSMMtube	muscle
34	chr11:86777000-86787000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr11:86777200-86786400	Weak transcription	Fetal Intestine Large	intestine
36	chr11:86777200-86786600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr11:86777400-86786600	Weak transcription	HMEC	breast
38	chr11:86777400-86786800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr11:86777400-86787600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:86777400-86792400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr11:86778000-86786800	Weak transcription	Primary B cells from cord blood	blood
42	chr11:86778000-86786800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr11:86778400-86786000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr11:86778400-86792400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:86778800-86789000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:86778800-86789600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr11:86778800-86791800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr11:86778800-86792400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr11:86779000-86786600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr11:86779000-86786600	Weak transcription	Rectal Smooth Muscle	rectum

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