Variant report

Variant	rs11631944
Chromosome Location	chr15:74472294-74472295
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	TFAP2C	chr15:74471553-74472823	Hela-S3	cervix:	n/a	n/a
2	TCF12	chr15:74471543-74472367	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr15:74471553-74472609	ECC-1	luminal epithelium:	n/a	n/a
4	GATA3	chr15:74471524-74472380	SK-N-SH	brain:	n/a	n/a
5	MYC	chr15:74471652-74472621	MCF10A-Er-Src	breast:	n/a	n/a
6	RXRA	chr15:74471616-74472691	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr15:74471562-74472298	A549	lung:	n/a	n/a
8	POLR2A	chr15:74472218-74472579	A549	lung:	n/a	n/a
9	PBX3	chr15:74471667-74472333	SK-N-SH	brain:	n/a	n/a
10	FOSL2	chr15:74471487-74472853	A549	lung:	n/a	chr15:74472604-74472614 chr15:74472604-74472614
11	ZBTB7A	chr15:74471321-74472346	ECC-1	luminal epithelium:	n/a	chr15:74471484-74471491
12	EP300	chr15:74471606-74472371	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr15:74471682-74472409	ECC-1	luminal epithelium:	n/a	n/a
14	TCF12	chr15:74471555-74472474	ECC-1	luminal epithelium:	n/a	n/a
15	EP300	chr15:74471685-74472299	A549	lung:	n/a	n/a
16	JUND	chr15:74469814-74473399	SK-N-SH	brain:	n/a	chr15:74472604-74472614 chr15:74472604-74472614 chr15:74470403-74470410
17	TCF12	chr15:74471542-74472827	A549	lung:	n/a	chr15:74472614-74472623
18	SMARCC1	chr15:74471538-74472549	Hela-S3	cervix:	n/a	n/a
19	NFIC	chr15:74471656-74472413	SK-N-SH	brain:	n/a	n/a
20	TCF12	chr15:74471570-74472526	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr15:74471881-74472460	Gliobla	brain:	n/a	n/a
22	MAX	chr15:74471664-74472567	SK-N-SH	brain:	n/a	n/a
23	MAZ	chr15:74471518-74472308	IMR90	lung:	n/a	n/a
24	RAD21	chr15:74471654-74472486	ECC-1	luminal epithelium:	n/a	n/a
25	PBX3	chr15:74471548-74472345	SK-N-SH	brain:	n/a	n/a
26	FOSL2	chr15:74471590-74472344	SK-N-SH	brain:	n/a	n/a
27	EP300	chr15:74471512-74472511	SK-N-SH	brain:	n/a	n/a
28	MAX	chr15:74471757-74472364	ECC-1	luminal epithelium:	n/a	n/a
29	RCOR1	chr15:74471334-74473039	IMR90	lung:	n/a	n/a
30	GTF2F1	chr15:74471675-74472383	Hela-S3	cervix:	n/a	n/a
31	MAX	chr15:74471536-74472972	A549	lung:	n/a	n/a
32	NFIC	chr15:74471540-74473134	SK-N-SH	brain:	n/a	n/a
33	GATA3	chr15:74471583-74472385	SK-N-SH	brain:	n/a	n/a
34	NFIC	chr15:74471546-74472576	ECC-1	luminal epithelium:	n/a	n/a
35	EP300	chr15:74471437-74472579	ECC-1	luminal epithelium:	n/a	n/a
36	TCF12	chr15:74471467-74473216	SK-N-SH	brain:	n/a	chr15:74472614-74472623 chr15:74471501-74471508
37	POLR2A	chr15:74471701-74472317	U87	brain:	n/a	n/a
38	TFAP2A	chr15:74471553-74472520	Hela-S3	cervix:	n/a	n/a
39	SMARCB1	chr15:74471544-74472762	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:74471188..74474733-chr15:74480852..74485546,5	MCF-7	breast:
2	chr15:74466900..74472644-chr15:74474380..74478364,5	K562	blood:
3	chr15:74466286..74468382-chr15:74470933..74472488,2	MCF-7	breast:
4	chr15:74465289..74467713-chr15:74468699..74473006,4	MCF-7	breast:
5	chr15:74471878..74474660-chr15:74491803..74495339,3	MCF-7	breast:

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

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11630317	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11630924	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs11631509	0.85[EUR][1000 genomes]
rs11639090	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11639369	0.82[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11854957	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11855667	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs11857410	0.82[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs12899173	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12907503	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12911581	0.84[EUR][1000 genomes]
rs12912258	0.82[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs12912578	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12913041	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12915891	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs13259	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2062309	0.96[EUR][1000 genomes]
rs2415169	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs2899824	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34147822	0.88[EUR][1000 genomes]
rs34573746	0.87[EUR][1000 genomes]
rs34868798	0.97[EUR][1000 genomes]
rs351242	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs35255788	0.88[EUR][1000 genomes]
rs35462746	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35661273	0.97[EUR][1000 genomes]
rs3848160	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3848161	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3888004	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs409856	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs5742915	1.00[CHD][hapmap]
rs62003660	0.88[EUR][1000 genomes]
rs62003661	0.85[EUR][1000 genomes]
rs62005707	0.97[EUR][1000 genomes]
rs62005709	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62005710	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62005711	0.93[EUR][1000 genomes]
rs71399778	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs733163	0.82[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs8037531	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs923118	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.97[EUR][1000 genomes]
rs9630417	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.96[EUR][1000 genomes]
rs971755	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs971756	0.82[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs971757	0.82[CEU][hapmap];0.89[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
rs11631944	C15orf39	cis	cerebellum	SCAN

Chromatin state (count:79 , 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	chr15:74467800-74472400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:74467800-74473600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr15:74468400-74473400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr15:74468400-74473600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr15:74468600-74473200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:74468600-74473600	Enhancers	NH-A	brain
16	chr15:74469000-74472800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:74469000-74473200	Enhancers	NHLF	lung
18	chr15:74469200-74473200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:74469200-74474000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr15:74469200-74491800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:74469400-74487600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:74469400-74493200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:74470000-74472600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:74470000-74472600	Enhancers	Brain Angular Gyrus	brain
25	chr15:74470000-74473000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:74470000-74473400	Enhancers	HUVEC	blood vessel
27	chr15:74470000-74473800	Enhancers	Left Ventricle	heart
28	chr15:74470600-74473600	Enhancers	Ovary	ovary
29	chr15:74470600-74474000	Enhancers	Lung	lung
30	chr15:74470600-74475600	Weak transcription	Fetal Kidney	kidney
31	chr15:74470600-74484000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:74470800-74492800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr15:74471000-74473600	Enhancers	Fetal Muscle Leg	muscle
34	chr15:74471200-74472400	Flanking Active TSS	Hela-S3	cervix
35	chr15:74471200-74472800	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr15:74471200-74473600	Enhancers	Fetal Thymus	thymus
37	chr15:74471200-74473600	Enhancers	HMEC	breast
38	chr15:74471200-74473800	Enhancers	Spleen	Spleen
39	chr15:74471400-74472400	Enhancers	Fetal Muscle Trunk	muscle
40	chr15:74471400-74472400	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr15:74471400-74472800	Enhancers	Rectal Smooth Muscle	rectum
42	chr15:74471400-74473200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:74471400-74473200	Enhancers	Fetal Lung	lung
44	chr15:74471400-74473400	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr15:74471400-74473800	Enhancers	Esophagus	oesophagus
46	chr15:74471400-74475200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:74471600-74472400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr15:74471600-74472400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:74471600-74472400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:74471600-74472400	Enhancers	Brain Anterior Caudate	brain

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