Variant report

Variant	rs4539561
Chromosome Location	chr15:73436922-73436923
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73433416..73435936-chr15:73436842..73439135,2	K562	blood:

Variant related genes	Relation type
ENSG00000259691	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1017809	1.00[GIH][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1029	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1038136	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11852881	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11853109	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11856383	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11856433	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11856466	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11857053	1.00[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12101540	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12101734	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13329282	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1382780	0.85[EUR][1000 genomes]
rs1678245	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16957661	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1714529	0.85[EUR][1000 genomes]
rs1714530	0.85[EUR][1000 genomes]
rs1714532	0.85[EUR][1000 genomes]
rs1812363	0.85[EUR][1000 genomes]
rs1842164	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1895842	1.00[GIH][hapmap]
rs1963253	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1963254	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1979410	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2169952	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2254390	0.82[EUR][1000 genomes]
rs2254818	0.82[EUR][1000 genomes]
rs2623990	0.82[EUR][1000 genomes]
rs2623996	0.85[EUR][1000 genomes]
rs2680347	0.85[EUR][1000 genomes]
rs2680351	0.85[EUR][1000 genomes]
rs28547177	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28572029	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28582318	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28645758	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs28676873	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28808999	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28828370	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4238459	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4287530	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4325518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4635304	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4776626	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4777584	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs524457	1.00[GIH][hapmap]
rs533460	1.00[GIH][hapmap]
rs55969660	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57453823	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6495054	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7176908	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7180017	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73438015	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7403367	1.00[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7497831	1.00[CEU][hapmap];0.90[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8031718	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8034243	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8034826	0.92[AFR][1000 genomes]
rs8035499	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs8035717	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8038411	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs899480	1.00[GIH][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9920152	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9920459	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9920675	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv904339	chr15:73375847-73483718	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv904340	chr15:73375847-73524629	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv904341	chr15:73390790-73483718	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904342	chr15:73390790-73524629	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active 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
10	nsv527236	chr15:73421239-73469535	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73396400-73444600	Weak transcription	Psoas Muscle	Psoas
2	chr15:73401400-73480200	Weak transcription	Right Ventricle	heart
3	chr15:73403000-73443400	Weak transcription	Fetal Kidney	kidney
4	chr15:73404200-73442600	Weak transcription	Left Ventricle	heart
5	chr15:73408000-73443400	Weak transcription	Adipose Nuclei	Adipose
6	chr15:73413200-73437200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:73413600-73446400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr15:73414000-73437000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:73414000-73440000	Weak transcription	Fetal Brain Female	brain
10	chr15:73414200-73445600	Weak transcription	Brain Substantia Nigra	brain
11	chr15:73414400-73458200	Weak transcription	Colonic Mucosa	Colon
12	chr15:73415400-73446600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:73416000-73453200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr15:73416600-73444600	Weak transcription	Fetal Muscle Leg	muscle
15	chr15:73416600-73444600	Weak transcription	Lung	lung
16	chr15:73416800-73448800	Weak transcription	Ovary	ovary
17	chr15:73417000-73443000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr15:73421000-73443200	Weak transcription	Brain Angular Gyrus	brain
19	chr15:73423400-73438200	Weak transcription	Brain Anterior Caudate	brain
20	chr15:73423400-73445400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:73423400-73448800	Weak transcription	Pancreas	Pancrea
22	chr15:73423600-73443200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr15:73423600-73444600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:73424200-73449200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:73425200-73447200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:73429000-73456600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:73429200-73449200	Weak transcription	Gastric	stomach
28	chr15:73429400-73447200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr15:73430200-73466600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:73431400-73443000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:73431800-73453800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr15:73432200-73437600	Weak transcription	Fetal Lung	lung
33	chr15:73432600-73448600	Weak transcription	Fetal Brain Male	brain
34	chr15:73433200-73440000	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr15:73434200-73438000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:73435000-73444600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr15:73435400-73437800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr15:73435600-73437000	Strong transcription	Brain Hippocampus Middle	brain
39	chr15:73435600-73439200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr15:73435600-73443200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr15:73435600-73447200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:73435800-73448800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr15:73436000-73438800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:73436000-73439400	Weak transcription	Aorta	Aorta
45	chr15:73436000-73443200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr15:73436000-73444600	Weak transcription	Fetal Stomach	stomach
47	chr15:73436000-73446400	Weak transcription	Liver	Liver
48	chr15:73436200-73437000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr15:73436200-73439800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr15:73436200-73443800	Weak transcription	Fetal Intestine Small	intestine

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