Variant report

Variant	rs11054439
Chromosome Location	chr12:11895308-11895309
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1009951	0.84[EUR][1000 genomes]
rs1009953	0.84[EUR][1000 genomes]
rs1009954	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs10743967	0.92[EUR][1000 genomes]
rs10845407	0.80[EUR][1000 genomes]
rs10845408	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11054421	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs11054423	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs11054424	0.87[EUR][1000 genomes]
rs11054429	0.89[EUR][1000 genomes]
rs11054433	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs11615175	0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12228191	0.81[EUR][1000 genomes]
rs12369491	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12828066	0.86[CHB][hapmap]
rs17818498	0.92[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17818624	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2051525	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs2187642	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs2416882	0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs2416883	0.89[JPT][hapmap]
rs2724588	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs2724616	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs2724618	0.90[EUR][1000 genomes]
rs2724633	0.96[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2724645	0.84[EUR][1000 genomes]
rs2724648	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs2856321	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs2856322	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs2856324	0.83[EUR][1000 genomes]
rs2856344	0.84[EUR][1000 genomes]
rs2900208	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2954980	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs4763719	0.84[EUR][1000 genomes]
rs4763720	0.81[EUR][1000 genomes]
rs4763721	0.81[EUR][1000 genomes]
rs7488701	0.81[EUR][1000 genomes]
rs762717	0.82[EUR][1000 genomes]
rs972798	0.89[JPT][hapmap];0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11873200-11902400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:11873200-11909400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:11880400-11896200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:11880600-11896400	Weak transcription	Fetal Stomach	stomach
5	chr12:11882400-11899200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:11882400-11902600	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:11882400-11903200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr12:11883600-11896200	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:11883800-11906000	Weak transcription	Liver	Liver
10	chr12:11884200-11896200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr12:11884200-11899000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:11885200-11906200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:11885600-11898600	Weak transcription	Primary T cells from cord blood	blood
14	chr12:11885600-11899000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:11885600-11905200	Weak transcription	Fetal Intestine Large	intestine
16	chr12:11885800-11896800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:11885800-11898400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:11885800-11911600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:11886000-11900000	Weak transcription	Colonic Mucosa	Colon
20	chr12:11886800-11897800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr12:11887800-11896400	Weak transcription	Dnd41	blood
22	chr12:11889800-11896800	Weak transcription	Fetal Kidney	kidney
23	chr12:11889800-11901800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr12:11890000-11902400	Weak transcription	Brain Hippocampus Middle	brain
25	chr12:11891200-11896000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:11891600-11896000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr12:11892000-11896400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:11892400-11896800	Weak transcription	Right Ventricle	heart
29	chr12:11892400-11898600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:11892600-11896600	Enhancers	Stomach Mucosa	stomach
31	chr12:11893000-11896800	Enhancers	Primary hematopoietic stem cells	blood
32	chr12:11893200-11915000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:11893400-11895400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:11893400-11895400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:11893400-11896400	Genic enhancers	GM12878-XiMat	blood
36	chr12:11893600-11895400	Enhancers	Thymus	Thymus
37	chr12:11893600-11897800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:11893800-11895400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:11893800-11895400	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr12:11893800-11895400	Enhancers	NHEK	skin
41	chr12:11893800-11896400	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr12:11893800-11901200	Enhancers	HMEC	breast
43	chr12:11894000-11896400	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr12:11894200-11896200	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr12:11894400-11896800	Weak transcription	Fetal Brain Male	brain
46	chr12:11894400-11897800	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr12:11894400-11898800	Weak transcription	Right Atrium	heart
48	chr12:11894400-11899000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr12:11894600-11895400	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr12:11894600-11895600	Enhancers	Pancreatic Islets	Pancreatic Islet

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