Variant report

Variant	rs62003661
Chromosome Location	chr15:74506479-74506480
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	NANOG	chr15:74506283-74506897	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr15:74505846-74506576	K562	blood:	n/a	n/a
3	SP1	chr15:74506147-74506681	H1-hESC	embryonic stem cell:	n/a	chr15:74506400-74506411 chr15:74506401-74506410 chr15:74506162-74506171
4	YY1	chr15:74506308-74506727	H1-hESC	embryonic stem cell:	n/a	chr15:74506401-74506412
5	ATF2	chr15:74506325-74506657	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr15:74505998-74506969	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF143	chr15:74506243-74507055	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr15:74506062-74507014	H1-hESC	embryonic stem cell:	n/a	n/a
9	SP4	chr15:74506310-74506606	H1-hESC	embryonic stem cell:	n/a	chr15:74506400-74506411
10	RAD21	chr15:74506191-74506642	H1-hESC	embryonic stem cell:	n/a	n/a
11	EGR1	chr15:74506242-74506689	H1-hESC	embryonic stem cell:	n/a	n/a
12	YY1	chr15:74506147-74506926	H1-hESC	embryonic stem cell:	n/a	chr15:74506401-74506412
13	HDAC2	chr15:74506184-74506658	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTBP2	chr15:74506044-74506727	H1-hESC	embryonic stem cell:	n/a	n/a
15	E2F6	chr15:74505944-74506780	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:74504672..74507489-chr15:74514073..74516992,2	MCF-7	breast:
2	chr15:74495538..74499115-chr15:74503082..74506667,3	MCF-7	breast:
3	chr15:74497610..74499444-chr15:74504967..74507735,2	K562	blood:
4	chr15:74502835..74504692-chr15:74505087..74506965,2	MCF-7	breast:

Variant related genes	Relation type
STRA6	TF binding region
ENSG00000259264	TF binding region
CCDC33	TF binding region
ENSG00000137868	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11630317	0.82[EUR][1000 genomes]
rs11630924	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11631509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11631944	0.85[EUR][1000 genomes]
rs11633687	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11639090	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11639369	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11854957	0.85[EUR][1000 genomes]
rs11857410	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12899173	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12905521	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12907503	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12911581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12912258	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12912578	0.86[EUR][1000 genomes]
rs12913041	0.86[EUR][1000 genomes]
rs12915891	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13259	0.85[EUR][1000 genomes]
rs2062309	0.83[EUR][1000 genomes]
rs2415169	0.84[EUR][1000 genomes]
rs2899824	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34004794	0.81[AMR][1000 genomes]
rs34147822	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34234753	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34573746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34591452	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34868798	0.84[EUR][1000 genomes]
rs34985083	0.81[AMR][1000 genomes]
rs35036456	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35255788	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35462746	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35661273	0.84[EUR][1000 genomes]
rs35917667	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3848160	0.85[EUR][1000 genomes]
rs3848161	0.85[EUR][1000 genomes]
rs3888004	0.85[EUR][1000 genomes]
rs409856	0.85[EUR][1000 genomes]
rs62003660	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62005707	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62005709	0.85[EUR][1000 genomes]
rs62005710	0.85[EUR][1000 genomes]
rs62005711	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71399778	0.85[EUR][1000 genomes]
rs72747610	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs733163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8037531	0.84[EUR][1000 genomes]
rs923118	0.84[EUR][1000 genomes]
rs9630417	0.83[EUR][1000 genomes]
rs971755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs971756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs971757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv904345	chr15:74458181-74526596	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv904347	chr15:74462629-74537101	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv904348	chr15:74462629-74542686	Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv471253	chr15:74489207-74545148	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv904349	chr15:74500105-74542686	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv904350	chr15:74500105-74548773	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74489200-74509600	Weak transcription	Gastric	stomach
2	chr15:74501200-74507400	Weak transcription	Spleen	Spleen
3	chr15:74501800-74507200	Weak transcription	HSMM	muscle
4	chr15:74502200-74508800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:74502400-74507400	Weak transcription	Placenta	Placenta
6	chr15:74503000-74506600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:74503000-74507000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:74503000-74507200	Weak transcription	Fetal Kidney	kidney
9	chr15:74503200-74507000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:74503200-74507000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:74503800-74507400	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr15:74504000-74508800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:74504000-74508800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr15:74504200-74507000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr15:74504200-74507200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr15:74504200-74508200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:74504200-74508600	Enhancers	HepG2	liver
18	chr15:74504200-74508800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:74504200-74508800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr15:74504400-74506800	Weak transcription	Hela-S3	cervix
21	chr15:74504400-74508400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:74504400-74508800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:74504400-74508800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:74504400-74508800	Enhancers	Fetal Thymus	thymus
25	chr15:74504400-74510400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:74504600-74507000	Enhancers	A549	lung
27	chr15:74504600-74507600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
28	chr15:74505200-74507000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:74505200-74508600	Enhancers	GM12878-XiMat	blood
30	chr15:74505600-74506800	Enhancers	K562	blood
31	chr15:74505600-74507600	Enhancers	H9 Cell Line	embryonic stem cell
32	chr15:74505600-74507600	Enhancers	Fetal Brain Male	brain
33	chr15:74505600-74508200	Enhancers	Fetal Muscle Trunk	muscle
34	chr15:74505800-74507600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr15:74505800-74507600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:74505800-74508400	Enhancers	Fetal Lung	lung
37	chr15:74505800-74508600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr15:74505800-74508600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr15:74505800-74508600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr15:74505800-74508600	Enhancers	Fetal Muscle Leg	muscle
41	chr15:74506000-74506600	Enhancers	Fetal Intestine Small	intestine
42	chr15:74506000-74506600	Enhancers	Left Ventricle	heart
43	chr15:74506000-74506600	Enhancers	Stomach Smooth Muscle	stomach
44	chr15:74506000-74506800	Enhancers	Fetal Heart	heart
45	chr15:74506000-74506800	Enhancers	Lung	lung
46	chr15:74506000-74507200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr15:74506000-74507600	Enhancers	Fetal Brain Female	brain
48	chr15:74506000-74507800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:74506000-74507800	Enhancers	Brain Germinal Matrix	brain
50	chr15:74506000-74508000	Enhancers	Fetal Stomach	stomach

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