Variant report

Variant	rs2341060
Chromosome Location	chr2:151479273-151479274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr2:151479191-151479472	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000232359	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10188741	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10432416	0.98[ASN][1000 genomes]
rs10497064	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497067	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10497068	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10497069	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10803803	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10930181	0.85[AFR][1000 genomes]
rs10930198	0.90[ASN][1000 genomes]
rs10930203	0.98[ASN][1000 genomes]
rs11894862	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11899711	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12052383	0.91[CHB][hapmap]
rs12473120	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614085	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs13019271	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16828368	0.91[CHB][hapmap]
rs16828372	0.90[CHB][hapmap]
rs2247416	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290815	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290816	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290817	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2341059	0.90[CHB][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341061	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341062	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341063	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341064	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341065	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341066	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341067	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2341068	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341071	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341072	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2341073	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2341074	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341075	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2341078	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341081	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341082	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341083	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341084	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341085	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341086	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341087	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341088	0.98[ASN][1000 genomes]
rs2341089	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341090	0.98[ASN][1000 genomes]
rs2341091	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2879931	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879932	0.85[AFR][1000 genomes]
rs4233665	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233666	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233667	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4297879	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4334493	0.91[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4365460	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4374370	0.91[AFR][1000 genomes]
rs4380232	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4408725	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4514872	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4530365	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4530366	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4600650	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4627564	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4664150	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664689	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664692	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710003	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6724645	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71338158	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7557930	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559963	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7560326	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562436	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7569499	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593427	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597424	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602198	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9287861	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9287862	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001838	chr2:150819672-151745876	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv535980	chr2:150819672-151745876	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv532473	chr2:151164210-151701860	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv834415	chr2:151374254-151558649	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv2757836	chr2:151457277-151844210	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv2759096	chr2:151457277-151844210	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151468200-151480000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:151470200-151480400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:151473000-151487000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:151473800-151479400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr2:151474000-151479600	Enhancers	NHDF-Ad	bronchial
6	chr2:151474200-151479400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:151474200-151479400	Enhancers	HMEC	breast
8	chr2:151474200-151479600	Enhancers	NH-A	brain
9	chr2:151474400-151480200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:151475600-151479400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:151476000-151479600	Enhancers	HUVEC	blood vessel
12	chr2:151476200-151479400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:151476200-151479400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr2:151476200-151479400	Enhancers	NHEK	skin
15	chr2:151476200-151479600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:151476200-151479600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:151476200-151479600	Enhancers	NHLF	lung
18	chr2:151476600-151479600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr2:151476600-151479600	Enhancers	HSMM	muscle
20	chr2:151476800-151480600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:151476800-151483400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:151476800-151485200	Weak transcription	Psoas Muscle	Psoas
23	chr2:151477000-151479400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:151477000-151480200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:151477400-151479400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:151477400-151479400	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr2:151477600-151479400	Enhancers	Fetal Lung	lung
28	chr2:151477600-151479400	Enhancers	Right Ventricle	heart
29	chr2:151477800-151479400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:151477800-151480400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:151478000-151479400	Enhancers	Hela-S3	cervix
32	chr2:151478400-151482000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:151478600-151479400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:151478600-151479400	Enhancers	Gastric	stomach
35	chr2:151478600-151479400	Enhancers	Left Ventricle	heart
36	chr2:151478800-151480400	Weak transcription	Adipose Nuclei	Adipose
37	chr2:151478800-151485200	Weak transcription	Aorta	Aorta
38	chr2:151479000-151480200	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:151479000-151480400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:151479000-151480400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:151479000-151480400	Weak transcription	Fetal Stomach	stomach
42	chr2:151479200-151479600	Enhancers	Brain Germinal Matrix	brain
43	chr2:151479200-151480000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr2:151479200-151480200	Weak transcription	HSMMtube	muscle
45	chr2:151479200-151480400	Weak transcription	Lung	lung
46	chr2:151479200-151480400	Weak transcription	Right Atrium	heart
47	chr2:151479200-151480400	Weak transcription	Osteobl	bone
48	chr2:151479200-151483000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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