Variant report

Variant	rs12417977
Chromosome Location	chr11:73251370-73251371
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10898921	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235736	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11235772	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235783	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235784	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235786	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235787	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235789	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235790	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235791	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235792	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235796	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235802	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235803	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11235807	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235810	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11235811	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11235816	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417351	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417890	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418558	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12420228	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421012	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17132126	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244589	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808095	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1939383	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087498	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34493385	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55885773	0.86[EUR][1000 genomes]
rs56277844	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56375530	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56394842	0.94[EUR][1000 genomes]
rs57225667	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60203229	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61018857	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1048171	chr11:73210060-73271831	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73240200-73252600	Weak transcription	Placenta	Placenta
2	chr11:73240400-73251600	Weak transcription	Fetal Intestine Large	intestine
3	chr11:73240400-73253800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:73240400-73254400	Weak transcription	Stomach Mucosa	stomach
5	chr11:73240600-73255400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr11:73241400-73251400	Weak transcription	Colon Smooth Muscle	Colon
7	chr11:73243400-73279600	Weak transcription	Fetal Stomach	stomach
8	chr11:73243800-73263000	Weak transcription	Fetal Intestine Small	intestine
9	chr11:73244000-73253000	Weak transcription	Psoas Muscle	Psoas
10	chr11:73246200-73256400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:73248600-73251400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:73248600-73251800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr11:73248800-73251600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:73248800-73251800	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr11:73249400-73251400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr11:73249400-73253400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr11:73249600-73252400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:73249600-73252800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr11:73249600-73253800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:73249600-73266000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr11:73249600-73266400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr11:73249600-73276000	Weak transcription	Fetal Muscle Leg	muscle
23	chr11:73249800-73251600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:73249800-73253000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:73249800-73253000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr11:73249800-73253400	Weak transcription	Small Intestine	intestine
27	chr11:73249800-73262600	Weak transcription	Brain Anterior Caudate	brain
28	chr11:73250000-73251600	Enhancers	Fetal Brain Female	brain
29	chr11:73250000-73251800	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr11:73250000-73252000	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr11:73250000-73252200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr11:73250000-73253400	Weak transcription	Fetal Heart	heart
33	chr11:73250000-73255000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr11:73250000-73255200	Weak transcription	HSMM	muscle
35	chr11:73250000-73261800	Weak transcription	Brain Substantia Nigra	brain
36	chr11:73250000-73262200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr11:73250000-73262600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:73250000-73262600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr11:73250000-73262800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr11:73250000-73265800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr11:73250000-73307800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr11:73250200-73251800	Enhancers	Primary T cells from cord blood	blood
43	chr11:73250200-73252600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr11:73250200-73253200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:73250200-73266400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:73250200-73278800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr11:73250800-73251400	Weak transcription	Right Ventricle	heart
48	chr11:73250800-73252000	Weak transcription	Spleen	Spleen
49	chr11:73250800-73252000	Enhancers	Dnd41	blood
50	chr11:73250800-73252200	Enhancers	Left Ventricle	heart

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