Variant report

Variant	rs11857410
Chromosome Location	chr15:74488424-74488425
allele	A/G
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	NR3C1	chr15:74488351-74489018	A549	lung:	n/a	n/a
2	EP300	chr15:74488300-74489127	SK-N-SH	brain:	n/a	chr15:74488842-74488858
3	TCF12	chr15:74488183-74489178	SK-N-SH	brain:	n/a	chr15:74488508-74488518
4	PBX3	chr15:74488275-74489102	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr15:74488282-74489164	SK-N-SH	brain:	n/a	n/a
6	ATF3	chr15:74488366-74488824	A549	lung:	n/a	n/a
7	RXRA	chr15:74488343-74489116	SK-N-SH	brain:	n/a	chr15:74488868-74488882
8	CEBPB	chr15:74488408-74489079	Hela-S3	cervix:	n/a	n/a
9	RCOR1	chr15:74488252-74489888	IMR90	lung:	n/a	n/a
10	SMARCC1	chr15:74488413-74489529	Hela-S3	cervix:	n/a	n/a
11	TCF12	chr15:74488211-74489030	SK-N-SH	brain:	n/a	chr15:74488508-74488518
12	NR3C1	chr15:74488193-74489113	A549	lung:	n/a	n/a
13	EP300	chr15:74488237-74489188	A549	lung:	n/a	chr15:74488842-74488858
14	RCOR1	chr15:74488396-74489065	Hela-S3	cervix:	n/a	n/a
15	SIN3AK20	chr15:74488244-74489169	MCF-7	breast:	n/a	n/a
16	TCF7L2	chr15:74488392-74489182	Hela-S3	cervix:	n/a	chr15:74489154-74489168
17	BCL3	chr15:74488346-74488987	A549	lung:	n/a	n/a
18	GATA3	chr15:74488298-74489164	SK-N-SH	brain:	n/a	n/a
19	RXRA	chr15:74488373-74489076	SK-N-SH	brain:	n/a	chr15:74488868-74488882
20	RAD21	chr15:74488423-74489050	Hela-S3	cervix:	n/a	chr15:74488873-74488885 chr15:74488873-74488883
21	REST	chr15:74488366-74488870	A549	lung:	n/a	n/a
22	TFAP2C	chr15:74488347-74489370	Hela-S3	cervix:	n/a	n/a
23	SP1	chr15:74488354-74489176	HCT-116	colon:	n/a	n/a
24	NFIC	chr15:74488210-74489139	SK-N-SH	brain:	n/a	n/a
25	MAZ	chr15:74488385-74489327	Hela-S3	cervix:	n/a	n/a
26	SP1	chr15:74488286-74489245	HCT-116	colon:	n/a	n/a
27	EP300	chr15:74488410-74488991	SK-N-SH_RA	brain:	n/a	chr15:74488842-74488858
28	FOSL2	chr15:74488320-74489009	A549	lung:	n/a	n/a
29	GATA3	chr15:74488267-74489235	A549	lung:	n/a	n/a
30	BRCA1	chr15:74488286-74488926	Hela-S3	cervix:	n/a	n/a
31	SP1	chr15:74488316-74489172	A549	lung:	n/a	n/a
32	PBX3	chr15:74488291-74489050	SK-N-SH	brain:	n/a	n/a
33	NFIC	chr15:74488424-74489089	ECC-1	luminal epithelium:	n/a	n/a
34	EP300	chr15:74488420-74488996	SK-N-SH_RA	brain:	n/a	chr15:74488842-74488858
35	TCF12	chr15:74488216-74489197	A549	lung:	n/a	chr15:74488508-74488518
36	MAX	chr15:74488239-74489157	A549	lung:	n/a	n/a
37	POLR2A	chr15:74488369-74488987	SK-N-SH	brain:	n/a	n/a
38	MAX	chr15:74488370-74489032	Hela-S3	cervix:	n/a	n/a
39	NFIC	chr15:74488356-74489045	SK-N-SH	brain:	n/a	n/a
40	CHD2	chr15:74488386-74488999	Hela-S3	cervix:	n/a	n/a
41	TCF7L2	chr15:74488411-74489059	HCT-116	colon:	n/a	n/a
42	SMC3	chr15:74488397-74489068	Hela-S3	cervix:	n/a	n/a
43	PBX3	chr15:74488343-74488838	A549	lung:	n/a	n/a
44	EP300	chr15:74488338-74489158	A549	lung:	n/a	chr15:74488842-74488858
45	SP1	chr15:74488354-74489165	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
ENSG00000259264	Chromatin interaction
ENSG00000137868	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11630317	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs11630924	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11631509	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11631944	0.82[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11633687	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11639090	0.88[EUR][1000 genomes]
rs11639369	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11854957	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs12899173	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs12905521	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12907503	0.91[EUR][1000 genomes]
rs12911581	0.81[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12912258	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12912578	0.82[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12913041	0.89[EUR][1000 genomes]
rs12915891	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13259	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs2062309	0.86[EUR][1000 genomes]
rs2415169	0.88[EUR][1000 genomes]
rs2899824	0.82[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs34147822	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34234753	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34573746	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34591452	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34868798	0.88[EUR][1000 genomes]
rs35036456	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35255788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35462746	0.87[EUR][1000 genomes]
rs35661273	0.88[EUR][1000 genomes]
rs35917667	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3848160	0.88[EUR][1000 genomes]
rs3848161	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs3888004	0.82[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs409856	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs5742915	1.00[CHD][hapmap]
rs62003660	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62003661	0.93[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	0.93[EUR][1000 genomes]
rs71399778	0.88[EUR][1000 genomes]
rs7179079	1.00[YRI][hapmap]
rs72747610	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs733163	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8037531	0.87[EUR][1000 genomes]
rs923118	1.00[CHD][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs9630417	1.00[CHD][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs971755	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs971756	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs971757	1.00[CEU][hapmap];0.93[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11857410	C15orf39	cis	cerebellum	SCAN

Chromatin state (count:70 , 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	chr15:74484000-74490000	Enhancers	HSMM	muscle
8	chr15:74484800-74488800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr15:74485000-74489800	Enhancers	NH-A	brain
10	chr15:74485400-74493000	Weak transcription	Fetal Thymus	thymus
11	chr15:74485800-74491000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:74485800-74492600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr15:74486000-74490200	Enhancers	Esophagus	oesophagus
14	chr15:74486400-74491400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:74486800-74488600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:74486800-74488600	Weak transcription	NHLF	lung
17	chr15:74487000-74488600	Weak transcription	NHEK	skin
18	chr15:74487200-74488800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr15:74487400-74489600	Enhancers	Spleen	Spleen
20	chr15:74487400-74490200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:74487400-74491600	Genic enhancers	Placenta	Placenta
22	chr15:74487600-74489400	Enhancers	Lung	lung
23	chr15:74487600-74489600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:74487600-74489600	Enhancers	Fetal Muscle Leg	muscle
25	chr15:74487600-74489800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:74487600-74489800	Enhancers	Fetal Heart	heart
27	chr15:74487600-74492600	Weak transcription	GM12878-XiMat	blood
28	chr15:74487800-74489400	Enhancers	Fetal Lung	lung
29	chr15:74487800-74489800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:74487800-74492600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr15:74488000-74489400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:74488000-74491200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr15:74488000-74492600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr15:74488000-74492800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr15:74488200-74489200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:74488200-74489200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr15:74488200-74489200	Enhancers	Left Ventricle	heart
38	chr15:74488200-74489200	Enhancers	Ovary	ovary
39	chr15:74488200-74489200	Flanking Active TSS	Hela-S3	cervix
40	chr15:74488200-74489400	Enhancers	Right Atrium	heart
41	chr15:74488200-74489400	Enhancers	Osteobl	bone
42	chr15:74488200-74489600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr15:74488200-74489600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:74488200-74489600	Enhancers	Duodenum Mucosa	Duodenum
45	chr15:74488200-74490000	Enhancers	HSMMtube	muscle
46	chr15:74488200-74490400	Enhancers	Fetal Intestine Large	intestine
47	chr15:74488200-74490400	Genic enhancers	Fetal Intestine Small	intestine
48	chr15:74488200-74491600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
49	chr15:74488400-74488600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:74488400-74488600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin

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