Variant report

Variant	rs11172799
Chromosome Location	chr12:59284551-59284552
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10506358	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs10877184	0.81[AFR][1000 genomes]
rs11172798	1.00[MEX][hapmap]
rs11172818	0.85[ASW][hapmap];0.87[YRI][hapmap]
rs12297238	1.00[MEX][hapmap]
rs12303283	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13377741	0.85[LWK][hapmap];0.97[MKK][hapmap];0.87[AFR][1000 genomes]
rs17121676	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17121678	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17121715	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs59360671	0.96[ASN][1000 genomes]
rs7303924	0.81[LWK][hapmap]
rs7957573	1.00[ASN][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	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers 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

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59262600-59295000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:59266000-59311000	Weak transcription	Fetal Thymus	thymus
3	chr12:59271600-59284600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:59271600-59284600	Strong transcription	Osteobl	bone
5	chr12:59272800-59285800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:59273600-59287000	Weak transcription	Stomach Mucosa	stomach
7	chr12:59273800-59289000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:59274800-59289000	Weak transcription	Right Ventricle	heart
9	chr12:59275000-59300800	Weak transcription	HSMMtube	muscle
10	chr12:59275200-59297800	Weak transcription	Hela-S3	cervix
11	chr12:59277400-59286000	Weak transcription	GM12878-XiMat	blood
12	chr12:59277800-59288800	Weak transcription	Right Atrium	heart
13	chr12:59279000-59286800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:59279000-59310800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:59279200-59290200	Weak transcription	Fetal Heart	heart
16	chr12:59279200-59309400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:59280200-59287400	Weak transcription	Psoas Muscle	Psoas
18	chr12:59281000-59289400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr12:59281200-59287400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:59281400-59284600	Enhancers	Brain Anterior Caudate	brain
21	chr12:59281600-59284600	Enhancers	Brain Angular Gyrus	brain
22	chr12:59282200-59284600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:59282200-59285600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:59282400-59286400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:59282400-59286800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:59282400-59287000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:59282400-59290200	Weak transcription	Fetal Brain Female	brain
28	chr12:59282400-59290600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:59282400-59297800	Weak transcription	A549	lung
30	chr12:59282800-59284600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:59282800-59287600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:59282800-59287800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr12:59283400-59284800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:59283400-59298000	Weak transcription	Fetal Brain Male	brain
35	chr12:59283800-59285000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:59283800-59285600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:59283800-59286800	Weak transcription	Brain Germinal Matrix	brain
38	chr12:59283800-59287200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:59283800-59288800	Weak transcription	Spleen	Spleen
40	chr12:59283800-59300400	Weak transcription	Placenta	Placenta
41	chr12:59284000-59285000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:59284000-59285600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr12:59284000-59285600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:59284000-59286400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:59284000-59286400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr12:59284000-59286600	Weak transcription	Colon Smooth Muscle	Colon
47	chr12:59284000-59286600	Strong transcription	HMEC	breast
48	chr12:59284000-59286800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:59284000-59286800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr12:59284000-59286800	Weak transcription	Small Intestine	intestine

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