Variant report

Variant	rs34147822
Chromosome Location	chr15:74488252-74488253
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	TCF12	chr15:74488183-74489178	SK-N-SH	brain:	n/a	chr15:74488508-74488518
2	RCOR1	chr15:74488252-74489888	IMR90	lung:	n/a	n/a
3	TCF12	chr15:74488211-74489030	SK-N-SH	brain:	n/a	chr15:74488508-74488518
4	NR3C1	chr15:74488193-74489113	A549	lung:	n/a	n/a
5	EP300	chr15:74488237-74489188	A549	lung:	n/a	chr15:74488842-74488858
6	SIN3AK20	chr15:74488244-74489169	MCF-7	breast:	n/a	n/a
7	NFIC	chr15:74488210-74489139	SK-N-SH	brain:	n/a	n/a
8	TCF12	chr15:74488216-74489197	A549	lung:	n/a	chr15:74488508-74488518
9	MAX	chr15:74488239-74489157	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:74481853..74488513-chr15:74489689..74497281,13	MCF-7	breast:
2	chr15:74483505..74486452-chr15:74486727..74489080,2	MCF-7	breast:
3	chr15:74473602..74475447-chr15:74485969..74488494,2	MCF-7	breast:

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

Extended variants
information (count: 58 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11630317	0.85[EUR][1000 genomes]
rs11630924	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11631509	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11631944	0.88[EUR][1000 genomes]
rs11633687	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11639090	0.88[EUR][1000 genomes]
rs11639369	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11854957	0.88[EUR][1000 genomes]
rs11857410	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12899173	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12905521	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12907503	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12911581	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12912258	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12912578	0.89[EUR][1000 genomes]
rs12913041	0.89[EUR][1000 genomes]
rs12915891	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13259	0.88[EUR][1000 genomes]
rs2062309	0.86[EUR][1000 genomes]
rs2415169	0.88[EUR][1000 genomes]
rs2899824	0.88[EUR][1000 genomes]
rs34004794	0.81[AMR][1000 genomes]
rs34234753	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34573746	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34591452	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34868798	0.88[EUR][1000 genomes]
rs34985083	0.81[AMR][1000 genomes]
rs35036456	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35255788	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35462746	0.87[EUR][1000 genomes]
rs35661273	0.88[EUR][1000 genomes]
rs35917667	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3848160	0.88[EUR][1000 genomes]
rs3848161	0.88[EUR][1000 genomes]
rs3888004	0.88[EUR][1000 genomes]
rs409856	0.90[EUR][1000 genomes]
rs62003660	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62003661	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62005707	0.88[EUR][1000 genomes]
rs62005709	0.88[EUR][1000 genomes]
rs62005710	0.88[EUR][1000 genomes]
rs62005711	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71399778	0.88[EUR][1000 genomes]
rs72747610	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs733163	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8037531	0.87[EUR][1000 genomes]
rs923118	0.88[EUR][1000 genomes]
rs9630417	0.86[EUR][1000 genomes]
rs971755	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs971756	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs971757	1.00[AMR][1000 genomes];0.99[EUR][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	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	nsv1050884	chr15:74394983-74489413	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74466200-74492800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:74469200-74491800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr15:74469400-74493200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:74470800-74492800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:74478600-74491400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:74480600-74491800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:74481000-74488400	Weak transcription	Right Ventricle	heart
8	chr15:74484000-74490000	Enhancers	HSMM	muscle
9	chr15:74484800-74488800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr15:74485000-74489800	Enhancers	NH-A	brain
11	chr15:74485400-74493000	Weak transcription	Fetal Thymus	thymus
12	chr15:74485800-74491000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:74485800-74492600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:74486000-74488400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:74486000-74490200	Enhancers	Esophagus	oesophagus
16	chr15:74486400-74488400	Weak transcription	NHDF-Ad	bronchial
17	chr15:74486400-74491400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr15:74486600-74488400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:74486600-74488400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:74486800-74488400	Weak transcription	HMEC	breast
21	chr15:74486800-74488600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr15:74486800-74488600	Weak transcription	NHLF	lung
23	chr15:74487000-74488400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:74487000-74488600	Weak transcription	NHEK	skin
25	chr15:74487200-74488800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr15:74487400-74488400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:74487400-74489600	Enhancers	Spleen	Spleen
28	chr15:74487400-74490200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr15:74487400-74491600	Genic enhancers	Placenta	Placenta
30	chr15:74487600-74489400	Enhancers	Lung	lung
31	chr15:74487600-74489600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:74487600-74489600	Enhancers	Fetal Muscle Leg	muscle
33	chr15:74487600-74489800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:74487600-74489800	Enhancers	Fetal Heart	heart
35	chr15:74487600-74492600	Weak transcription	GM12878-XiMat	blood
36	chr15:74487800-74489400	Enhancers	Fetal Lung	lung
37	chr15:74487800-74489800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:74487800-74492600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr15:74488000-74488400	Enhancers	Fetal Kidney	kidney
40	chr15:74488000-74488400	Weak transcription	Fetal Stomach	stomach
41	chr15:74488000-74488400	Transcr. at gene 5' and 3'	A549	lung
42	chr15:74488000-74489400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:74488000-74491200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:74488000-74492600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr15:74488000-74492800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr15:74488200-74488400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:74488200-74489200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:74488200-74489200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:74488200-74489200	Enhancers	Left Ventricle	heart
50	chr15:74488200-74489200	Enhancers	Ovary	ovary

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