Variant report

Variant	rs11172801
Chromosome Location	chr12:59287980-59287981
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1020031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877182	0.86[EUR][1000 genomes]
rs10877183	0.86[EUR][1000 genomes]
rs10877185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172795	0.81[EUR][1000 genomes]
rs11172797	0.86[EUR][1000 genomes]
rs11172802	0.92[EUR][1000 genomes]
rs11172804	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11172805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172806	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11172807	0.92[EUR][1000 genomes]
rs11172808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172809	0.92[EUR][1000 genomes]
rs11172811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172812	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172816	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172818	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12146851	0.95[EUR][1000 genomes]
rs17120227	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17617428	0.81[EUR][1000 genomes]
rs2167030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];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:93 , 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	chr12:59273800-59289000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:59274800-59289000	Weak transcription	Right Ventricle	heart
5	chr12:59275000-59300800	Weak transcription	HSMMtube	muscle
6	chr12:59275200-59297800	Weak transcription	Hela-S3	cervix
7	chr12:59277800-59288800	Weak transcription	Right Atrium	heart
8	chr12:59279000-59310800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:59279200-59290200	Weak transcription	Fetal Heart	heart
10	chr12:59279200-59309400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:59281000-59289400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr12:59282400-59290200	Weak transcription	Fetal Brain Female	brain
13	chr12:59282400-59290600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:59282400-59297800	Weak transcription	A549	lung
15	chr12:59283400-59298000	Weak transcription	Fetal Brain Male	brain
16	chr12:59283800-59288800	Weak transcription	Spleen	Spleen
17	chr12:59283800-59300400	Weak transcription	Placenta	Placenta
18	chr12:59284000-59288600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:59284000-59288600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr12:59284000-59288800	Weak transcription	Aorta	Aorta
21	chr12:59284000-59288800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr12:59284000-59288800	Weak transcription	Left Ventricle	heart
23	chr12:59284000-59294800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:59284000-59297800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:59284000-59297800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:59284000-59298000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:59284000-59298000	Weak transcription	HSMM	muscle
28	chr12:59284000-59300800	Weak transcription	Colonic Mucosa	Colon
29	chr12:59284000-59300800	Weak transcription	HepG2	liver
30	chr12:59284200-59288200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr12:59284200-59288600	Weak transcription	HUVEC	blood vessel
32	chr12:59284200-59289000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr12:59284200-59290200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:59284200-59297800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr12:59284200-59297800	Weak transcription	Liver	Liver
36	chr12:59284200-59304600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr12:59284600-59298000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:59285000-59290400	Enhancers	Brain Cingulate Gyrus	brain
39	chr12:59285600-59288600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:59285600-59292400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr12:59286000-59290000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr12:59286000-59292600	Enhancers	NHEK	skin
43	chr12:59286200-59288000	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr12:59286200-59289400	Strong transcription	Fetal Intestine Large	intestine
45	chr12:59286400-59289000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:59286400-59291000	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr12:59286600-59288200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:59286600-59289000	Genic enhancers	HMEC	breast
49	chr12:59286600-59292000	Enhancers	Colon Smooth Muscle	Colon
50	chr12:59286800-59288000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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