Variant report

Variant	rs1554120
Chromosome Location	chr3:150935371-150935372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1017348	0.89[CEU][hapmap]
rs10513387	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513393	0.88[CEU][hapmap]
rs1221002	0.89[CEU][hapmap]
rs13321176	0.88[CEU][hapmap]
rs13322794	0.94[CEU][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549829	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17204437	0.88[CEU][hapmap]
rs17282940	0.83[CEU][hapmap]
rs17282947	0.83[CEU][hapmap]
rs17290219	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17304673	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1920393	1.00[ASN][1000 genomes]
rs1920397	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2567325	0.83[CEU][hapmap]
rs55936523	1.00[AFR][1000 genomes]
rs6773020	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792089	0.88[CEU][hapmap]
rs722133	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155751	1.00[ASN][1000 genomes]
rs73155773	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155774	0.91[EUR][1000 genomes]
rs73155776	1.00[AFR][1000 genomes]
rs7614811	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814936	0.88[CEU][hapmap]
rs9817216	0.88[CEU][hapmap];1.00[ASN][1000 genomes]
rs9818251	0.92[CEU][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819885	0.88[CEU][hapmap]
rs9821749	1.00[ASN][1000 genomes]
rs9821937	0.83[CEU][hapmap];1.00[ASN][1000 genomes]
rs9831242	0.88[CEU][hapmap]
rs9836053	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838990	0.83[CEU][hapmap]
rs9848789	0.88[CEU][hapmap]
rs9850762	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854017	0.83[CEU][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9854126	0.94[CEU][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856118	0.83[CEU][hapmap]
rs9859854	0.83[CEU][hapmap]
rs9868643	0.82[CEU][hapmap]
rs9871229	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9871624	0.94[CEU][hapmap]
rs9872645	0.88[CEU][hapmap]
rs9876268	0.88[CEU][hapmap]
rs9876933	0.83[CEU][hapmap]
rs9881116	0.94[CEU][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Heschl's gyrus morphology	25130324	GWAS catalog

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150878000-150946000	Weak transcription	Placenta	Placenta
2	chr3:150928200-150936000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:150928800-150943800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:150928800-150946200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:150928800-150952800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:150928800-150953000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:150929000-150938200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:150929000-150943200	Weak transcription	Psoas Muscle	Psoas
9	chr3:150929000-150945200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr3:150929200-150938000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:150929200-150945400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:150929600-150939200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:150931400-150936000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:150932200-150936800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:150932200-150942800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:150932400-150937400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:150932400-150938200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:150932600-150946200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:150933200-150935600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:150933400-150937200	Strong transcription	Primary B cells from cord blood	blood
21	chr3:150933400-150937600	Enhancers	NHDF-Ad	bronchial
22	chr3:150933400-150937800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:150933600-150935400	Enhancers	Adipose Nuclei	Adipose
24	chr3:150933600-150937200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:150933600-150937400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:150933600-150937600	Enhancers	NH-A	brain
27	chr3:150933600-150937600	Enhancers	NHLF	lung
28	chr3:150933800-150936800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:150934000-150935400	Enhancers	Brain Anterior Caudate	brain
30	chr3:150934200-150935400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:150934200-150935600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:150934200-150937400	Enhancers	Osteobl	bone
33	chr3:150934400-150935400	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr3:150934400-150935800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:150934600-150935400	Enhancers	Aorta	Aorta
36	chr3:150934600-150935400	Enhancers	Rectal Smooth Muscle	rectum
37	chr3:150934600-150935600	Enhancers	Fetal Stomach	stomach
38	chr3:150934600-150937000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr3:150934600-150937200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:150934600-150939000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:150934800-150935400	Enhancers	HSMMtube	muscle
42	chr3:150934800-150936000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:150935000-150935400	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr3:150935000-150935600	Weak transcription	Colon Smooth Muscle	Colon
45	chr3:150935000-150935600	Enhancers	Left Ventricle	heart
46	chr3:150935000-150935800	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr3:150935000-150936200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:150935000-150938200	Enhancers	Fetal Heart	heart
49	chr3:150935200-150935400	Enhancers	H1 Cell Line	embryonic stem cell
50	chr3:150935200-150935400	Enhancers	Esophagus	oesophagus

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