Variant report

Variant	rs664936
Chromosome Location	chr15:59064786-59064787
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	REST	chr15:59062530-59064976	H1-neurons	neurons:	n/a	chr15:59063494-59063504 chr15:59063560-59063578 chr15:59064487-59064500
2	MXI1	chr15:59062083-59065755	SK-N-SH	brain:	n/a	chr15:59063345-59063354 chr15:59063345-59063354 chr15:59063347-59063356
3	JUN	chr15:59062762-59065164	K562	blood:	n/a	chr15:59063580-59063589
4	MYC	chr15:59062548-59065214	A549	lung:	n/a	chr15:59063346-59063355 chr15:59063346-59063356 chr15:59063345-59063356 chr15:59063346-59063355 chr15:59063345-59063355 chr15:59063346-59063355 chr15:59063345-59063356 chr15:59063348-59063357

No.	Distal block	Cell Line	Cell type
1	chr15:59064130..59065710-chr15:59066898..59069288,2	MCF-7	breast:
2	chr15:58622254..58626014-chr15:59062445..59064794,4	K562	blood:
3	chr15:59063628..59066119-chr15:59070101..59071953,2	MCF-7	breast:
4	chr15:59040077..59045685-chr15:59061303..59067063,14	K562	blood:
5	chr15:59064062..59066974-chr15:59068078..59069600,2	MCF-7	breast:
6	chr15:59061037..59064884-chr15:59224205..59227723,8	K562	blood:
7	chr15:59038832..59043387-chr15:59060936..59065101,7	K562	blood:

Variant related genes	Relation type
ENSG00000245975	TF binding region
ENSG00000137845	Chromatin interaction
ENSG00000128918	Chromatin interaction
ENSG00000137776	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11071397	0.85[JPT][hapmap]
rs12437928	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes]
rs12438114	0.81[EUR][1000 genomes]
rs12439632	0.80[JPT][hapmap]
rs12591310	0.85[JPT][hapmap]
rs12594276	0.86[EUR][1000 genomes]
rs12900320	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12901817	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12914164	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[EUR][1000 genomes]
rs1365772	0.90[TSI][hapmap]
rs1551445	0.85[JPT][hapmap]
rs1678977	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1869133	0.80[CEU][hapmap];0.87[TSI][hapmap]
rs1869135	0.80[CEU][hapmap];0.85[TSI][hapmap]
rs2620360	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28533385	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28549775	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28812884	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34362744	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs347112	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34880782	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3764196	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs4774311	0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs4775095	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs481309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs500057	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs501165	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs510759	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs556256	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs561903	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs574683	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs596094	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs597112	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs601795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs624536	0.86[EUR][1000 genomes]
rs625312	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs652193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs654857	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs654870	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs684505	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs688343	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7164053	0.82[AFR][1000 genomes]
rs7164844	0.89[LWK][hapmap];0.98[MKK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs7169205	0.85[JPT][hapmap]
rs7170538	0.89[LWK][hapmap];0.93[MKK][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes]
rs7171198	0.80[YRI][hapmap];0.82[AFR][1000 genomes]
rs7178970	0.84[AFR][1000 genomes]
rs8029301	0.85[JPT][hapmap]
rs8032298	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9744045	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	esv1843037	chr15:59005922-59115159	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	esv1826703	chr15:59005922-59213678	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	esv1798487	chr15:59027139-59213678	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	42 gene(s)	inside rSNPs	diseases
7	nsv428638	chr15:59032300-59126567	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59062200-59064800	Active TSS	HMEC	breast
2	chr15:59062200-59065000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:59062200-59065000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr15:59062200-59065000	Active TSS	K562	blood
5	chr15:59062200-59065400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr15:59062200-59066000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr15:59062200-59066000	Active TSS	NHLF	lung
8	chr15:59062200-59066200	Active TSS	HSMMtube	muscle
9	chr15:59062200-59067800	Active TSS	GM12878-XiMat	blood
10	chr15:59062400-59064800	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr15:59062400-59064800	Active TSS	Brain Substantia Nigra	brain
12	chr15:59062400-59065200	Active TSS	Brain Hippocampus Middle	brain
13	chr15:59062400-59065400	Active TSS	Brain Germinal Matrix	brain
14	chr15:59062400-59065800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr15:59062400-59065800	Active TSS	Psoas Muscle	Psoas
16	chr15:59062400-59066000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:59062400-59066200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:59062400-59066400	Active TSS	Right Ventricle	heart
19	chr15:59062400-59066600	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr15:59062400-59067400	Active TSS	Right Atrium	heart
21	chr15:59062400-59067800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr15:59062600-59064800	Active TSS	H9 Cell Line	embryonic stem cell
23	chr15:59062600-59064800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:59062600-59064800	Active TSS	Fetal Muscle Trunk	muscle
25	chr15:59062600-59065000	Active TSS	Brain Anterior Caudate	brain
26	chr15:59062600-59065000	Active TSS	Stomach Mucosa	stomach
27	chr15:59062600-59065400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:59062600-59065600	Active TSS	Colonic Mucosa	Colon
29	chr15:59062600-59065800	Active TSS	H1 Cell Line	embryonic stem cell
30	chr15:59062600-59065800	Active TSS	Aorta	Aorta
31	chr15:59062600-59065800	Active TSS	Left Ventricle	heart
32	chr15:59062600-59066000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:59062600-59066400	Active TSS	Ovary	ovary
34	chr15:59062800-59064800	Active TSS	Brain Angular Gyrus	brain
35	chr15:59062800-59064800	Active TSS	Brain Cingulate Gyrus	brain
36	chr15:59062800-59064800	Active TSS	Fetal Intestine Small	intestine
37	chr15:59062800-59064800	Active TSS	A549	lung
38	chr15:59062800-59065200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:59062800-59065600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:59062800-59065600	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr15:59062800-59065600	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr15:59062800-59065800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:59062800-59066800	Active TSS	NHDF-Ad	bronchial
44	chr15:59062800-59067000	Active TSS	Stomach Smooth Muscle	stomach
45	chr15:59063000-59064800	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr15:59063000-59064800	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr15:59063000-59064800	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr15:59063000-59064800	Active TSS	Fetal Intestine Large	intestine
49	chr15:59063000-59064800	Active TSS	Fetal Kidney	kidney
50	chr15:59063000-59065000	Active TSS	Fetal Muscle Leg	muscle

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