Variant report

Variant	rs12273408
Chromosome Location	chr11:86791309-86791310
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1026410	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898592	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10898598	0.95[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	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11234934	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11234935	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11234936	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11234949	0.91[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	0.81[ASN][1000 genomes]
rs11234979	0.81[ASN][1000 genomes]
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]
rs12273779	0.88[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	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12282651	0.96[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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12283210	0.81[ASN][1000 genomes]
rs12285441	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12286127	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12286867	0.98[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	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12289267	0.88[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	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17758940	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17759040	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2220472	0.81[ASN][1000 genomes]
rs28822396	0.81[ASN][1000 genomes]
rs35036190	0.81[ASN][1000 genomes]
rs4315108	0.81[ASN][1000 genomes]
rs4578415	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4594023	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55790509	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56028118	0.81[AMR][1000 genomes]
rs56880471	0.81[ASN][1000 genomes]
rs57664476	0.96[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]
rs58190299	0.81[ASN][1000 genomes]
rs60711353	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61904170	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61904173	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61904180	0.96[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	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7115725	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
11	nsv468776	chr11:86788716-86826422	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv555706	chr11:86788716-86826422	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86769200-86792400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr11:86770400-86808200	Weak transcription	HUVEC	blood vessel
3	chr11:86773000-86792000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr11:86774600-86792400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr11:86774800-86806400	Weak transcription	Small Intestine	intestine
6	chr11:86775600-86791400	Weak transcription	HSMM	muscle
7	chr11:86776400-86792400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr11:86776600-86793000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:86776600-86815600	Weak transcription	HSMMtube	muscle
10	chr11:86777400-86792400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr11:86778400-86792400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr11:86778800-86791800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr11:86778800-86792400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr11:86779400-86792400	Weak transcription	GM12878-XiMat	blood
15	chr11:86779600-86792200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr11:86782600-86795400	Weak transcription	Fetal Heart	heart
17	chr11:86783000-86814000	Weak transcription	Hela-S3	cervix
18	chr11:86783200-86799000	Weak transcription	Psoas Muscle	Psoas
19	chr11:86784000-86792000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr11:86786400-86791400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:86787200-86791800	Weak transcription	Colonic Mucosa	Colon
22	chr11:86787200-86794200	Weak transcription	Brain Anterior Caudate	brain
23	chr11:86787200-86795400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:86787400-86819600	Weak transcription	NH-A	brain
25	chr11:86787600-86791800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr11:86787600-86792000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr11:86787600-86804200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr11:86787600-86825200	Weak transcription	Brain Substantia Nigra	brain
29	chr11:86787800-86792400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr11:86787800-86792400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:86787800-86797200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:86787800-86797200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:86787800-86798200	Weak transcription	Spleen	Spleen
34	chr11:86787800-86804000	Weak transcription	Fetal Intestine Large	intestine
35	chr11:86787800-86817400	Weak transcription	Colon Smooth Muscle	Colon
36	chr11:86787800-86819400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr11:86788000-86792400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr11:86788000-86792400	Weak transcription	Ovary	ovary
39	chr11:86788000-86792800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr11:86788000-86795400	Weak transcription	Lung	lung
41	chr11:86788000-86797200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr11:86788000-86797200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr11:86788000-86797200	Weak transcription	Esophagus	oesophagus
44	chr11:86788000-86797200	Weak transcription	Fetal Intestine Small	intestine
45	chr11:86788000-86797200	Weak transcription	Fetal Thymus	thymus
46	chr11:86788000-86797200	Weak transcription	Thymus	Thymus
47	chr11:86788000-86798400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr11:86788000-86800000	Weak transcription	Brain Germinal Matrix	brain
49	chr11:86788000-86800000	Weak transcription	Gastric	stomach
50	chr11:86788000-86803200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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