Variant report

Variant	rs351242
Chromosome Location	chr15:74472716-74472717
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	CTCF	chr15:74472680-74472830	HCPEpiC	choroid plexus:	n/a	n/a
2	CTCF	chr15:74472640-74472790	HRE	kidney:	n/a	n/a
3	CTCF	chr15:74472600-74472810	GM06990	blood:	n/a	n/a
4	TFAP2C	chr15:74471553-74472823	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr15:74472680-74472830	HRE	kidney:	n/a	n/a
6	CTCF	chr15:74472620-74472770	GM12871	blood:	n/a	n/a
7	CTCF	chr15:74472640-74472790	HCFaa	heart:	n/a	n/a
8	CTCF	chr15:74472616-74472815	ProgFib	skin:	n/a	n/a
9	CTCF	chr15:74472640-74472790	HBMEC	blood vessel:	n/a	n/a
10	RAD21	chr15:74472615-74472804	H1-hESC	embryonic stem cell:	n/a	n/a
11	FOXA2	chr15:74472490-74472757	A549	lung:	n/a	n/a
12	FOS	chr15:74472453-74473157	HUVEC	blood vessel:	n/a	chr15:74472604-74472614 chr15:74472604-74472614
13	CTCF	chr15:74472660-74472810	HCM	heart:	n/a	n/a
14	FOSL2	chr15:74471487-74472853	A549	lung:	n/a	chr15:74472604-74472614 chr15:74472604-74472614
15	CTCF	chr15:74472620-74472770	AG04449	skin:	n/a	n/a
16	CTCF	chr15:74472600-74472750	AoAF	blood vessel:	n/a	n/a
17	CTCF	chr15:74472620-74472770	BJ	skin:	n/a	n/a
18	CTCF	chr15:74472620-74472770	WERI-Rb-1	eye:	n/a	n/a
19	CTCF	chr15:74472600-74472750	GM12866	blood:	n/a	n/a
20	CTCF	chr15:74472600-74472750	HUVEC	blood vessel:	n/a	n/a
21	CTCF	chr15:74472620-74472770	AoAF	blood vessel:	n/a	n/a
22	CTCF	chr15:74472660-74472810	HPAF	blood vessel:	n/a	n/a
23	CTCF	chr15:74472640-74472790	HPAF	blood vessel:	n/a	n/a
24	CTCF	chr15:74472700-74472850	HepG2	liver:	n/a	n/a
25	JUND	chr15:74469814-74473399	SK-N-SH	brain:	n/a	chr15:74472604-74472614 chr15:74472604-74472614 chr15:74470403-74470410
26	FOXA2	chr15:74472300-74472914	A549	lung:	n/a	n/a
27	MYC	chr15:74472365-74472801	MCF10A-Er-Src	breast:	n/a	n/a
28	GATA2	chr15:74472637-74473235	HUVEC	blood vessel:	n/a	chr15:74473010-74473020 chr15:74472822-74472832
29	CTCF	chr15:74472640-74472790	HCPEpiC	choroid plexus:	n/a	n/a
30	TCF12	chr15:74471542-74472827	A549	lung:	n/a	chr15:74472614-74472623
31	CTCF	chr15:74472600-74472750	AG04449	skin:	n/a	n/a
32	POLR2A	chr15:74472692-74472833	A549	lung:	n/a	n/a
33	CTCF	chr15:74472640-74472790	BJ	skin:	n/a	n/a
34	FOS	chr15:74472367-74472748	MCF10A-Er-Src	breast:	n/a	chr15:74472604-74472614 chr15:74472604-74472614
35	RAD21	chr15:74472445-74472893	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr15:74472600-74472750	HCM	heart:	n/a	n/a
37	CTCF	chr15:74472600-74472750	GM12865	blood:	n/a	n/a
38	FOS	chr15:74472455-74472898	MCF10A-Er-Src	breast:	n/a	chr15:74472604-74472614 chr15:74472604-74472614
39	CTCF	chr15:74472640-74472790	GM06990	blood:	n/a	n/a
40	FOS	chr15:74472455-74472787	MCF10A-Er-Src	breast:	n/a	chr15:74472604-74472614 chr15:74472604-74472614
41	CTCF	chr15:74472620-74472770	HA-sp	spinal cord:	n/a	n/a
42	RCOR1	chr15:74471334-74473039	IMR90	lung:	n/a	n/a
43	CTCF	chr15:74472580-74472730	GM12875	blood:	n/a	n/a
44	MAX	chr15:74471536-74472972	A549	lung:	n/a	n/a
45	NFIC	chr15:74471540-74473134	SK-N-SH	brain:	n/a	n/a
46	CTCF	chr15:74472620-74472770	HMF	breast:	n/a	n/a
47	MAZ	chr15:74472491-74472755	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr15:74472704-74472758	ProgFib	skin:	n/a	n/a
49	CTCF	chr15:74472630-74472782	GM12891	blood:	n/a	n/a
50	CTCF	chr15:74472640-74472790	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:74471188..74474733-chr15:74480852..74485546,5	MCF-7	breast:
2	chr15:74465289..74467713-chr15:74468699..74473006,4	MCF-7	breast:
3	chr15:74471878..74474660-chr15:74491803..74495339,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261543	TF binding region
ENSG00000129009	Chromatin interaction
ENSG00000137868	Chromatin interaction
ENSG00000259264	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11630317	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs11631944	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11633687	0.86[EUR][1000 genomes]
rs11639090	0.83[EUR][1000 genomes]
rs11854957	1.00[CEU][hapmap]
rs12899173	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12905521	0.86[EUR][1000 genomes]
rs12907503	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12912578	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12913041	0.84[EUR][1000 genomes]
rs12915891	0.85[CEU][hapmap]
rs13259	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2062309	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2415169	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs2899824	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs34234753	0.86[EUR][1000 genomes]
rs34591452	0.86[EUR][1000 genomes]
rs34868798	0.84[EUR][1000 genomes]
rs35036456	0.86[EUR][1000 genomes]
rs35462746	0.81[EUR][1000 genomes]
rs35661273	0.82[EUR][1000 genomes]
rs35917667	0.86[EUR][1000 genomes]
rs3848160	0.83[EUR][1000 genomes]
rs3848161	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3888004	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs409856	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs62005707	0.82[EUR][1000 genomes]
rs62005709	0.83[EUR][1000 genomes]
rs62005710	0.83[EUR][1000 genomes]
rs71399778	0.83[EUR][1000 genomes]
rs72747610	0.86[EUR][1000 genomes]
rs8037531	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs923118	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs9630417	0.86[CEU][hapmap];0.81[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:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74464800-74473600	Enhancers	Right Ventricle	heart
2	chr15:74465200-74473000	Enhancers	Brain Germinal Matrix	brain
3	chr15:74466200-74492800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:74466600-74473200	Enhancers	HSMMtube	muscle
5	chr15:74466600-74480600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr15:74467200-74473600	Enhancers	Right Atrium	heart
7	chr15:74467400-74473400	Genic enhancers	Fetal Stomach	stomach
8	chr15:74467400-74473800	Enhancers	NHDF-Ad	bronchial
9	chr15:74467600-74473200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:74467800-74473600	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr15:74468400-74473400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr15:74468400-74473600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr15:74468600-74473200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:74468600-74473600	Enhancers	NH-A	brain
15	chr15:74469000-74472800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:74469000-74473200	Enhancers	NHLF	lung
17	chr15:74469200-74473200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:74469200-74474000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr15:74469200-74491800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:74469400-74487600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr15:74469400-74493200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr15:74470000-74473000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:74470000-74473400	Enhancers	HUVEC	blood vessel
24	chr15:74470000-74473800	Enhancers	Left Ventricle	heart
25	chr15:74470600-74473600	Enhancers	Ovary	ovary
26	chr15:74470600-74474000	Enhancers	Lung	lung
27	chr15:74470600-74475600	Weak transcription	Fetal Kidney	kidney
28	chr15:74470600-74484000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:74470800-74492800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr15:74471000-74473600	Enhancers	Fetal Muscle Leg	muscle
31	chr15:74471200-74472800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr15:74471200-74473600	Enhancers	Fetal Thymus	thymus
33	chr15:74471200-74473600	Enhancers	HMEC	breast
34	chr15:74471200-74473800	Enhancers	Spleen	Spleen
35	chr15:74471400-74472800	Enhancers	Rectal Smooth Muscle	rectum
36	chr15:74471400-74473200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:74471400-74473200	Enhancers	Fetal Lung	lung
38	chr15:74471400-74473400	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr15:74471400-74473800	Enhancers	Esophagus	oesophagus
40	chr15:74471400-74475200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:74471600-74472800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr15:74471600-74473000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:74471600-74473200	Enhancers	Brain Cingulate Gyrus	brain
44	chr15:74471800-74473400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:74471800-74473600	Enhancers	Fetal Brain Female	brain
46	chr15:74471800-74478000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr15:74472000-74477400	Genic enhancers	Placenta	Placenta
48	chr15:74472200-74472800	Enhancers	Brain Substantia Nigra	brain
49	chr15:74472200-74473400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:74472200-74473600	Enhancers	Pancreas	Pancrea

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