Variant report

Variant	rs923118
Chromosome Location	chr15:74466271-74466272
allele	G/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	ZNF263	chr15:74466192-74466516	HEK293-T-REx	kidney:	n/a	chr15:74466371-74466380
2	POLR2A	chr15:74466073-74467011	ProgFib	skin:	n/a	n/a
3	POLR2A	chr15:74460105-74471859	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74465289..74467713-chr15:74468699..74473006,4	MCF-7	breast:

Variant related genes	Relation type
ISLR	TF binding region
ENSG00000261543	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11630317	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs11630924	0.88[EUR][1000 genomes]
rs11631509	0.84[EUR][1000 genomes]
rs11631944	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.97[EUR][1000 genomes]
rs11639090	0.99[EUR][1000 genomes]
rs11639369	1.00[CHD][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs11854957	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs11855667	0.85[EUR][1000 genomes]
rs11857410	1.00[CHD][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs12899173	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs12907503	0.95[EUR][1000 genomes]
rs12911581	0.84[EUR][1000 genomes]
rs12912258	0.82[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs12912578	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.98[EUR][1000 genomes]
rs12913041	0.98[EUR][1000 genomes]
rs12915891	0.83[CEU][hapmap];0.91[EUR][1000 genomes]
rs13259	0.91[CEU][hapmap];0.99[EUR][1000 genomes]
rs2062309	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2415169	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2899824	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.99[EUR][1000 genomes]
rs34147822	0.88[EUR][1000 genomes]
rs34573746	0.87[EUR][1000 genomes]
rs34868798	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs351242	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs35255788	0.88[EUR][1000 genomes]
rs35462746	0.97[EUR][1000 genomes]
rs35661273	0.98[EUR][1000 genomes]
rs3848160	0.99[EUR][1000 genomes]
rs3848161	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.99[EUR][1000 genomes]
rs3888004	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.99[EUR][1000 genomes]
rs409856	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs5742915	1.00[CHD][hapmap]
rs62003660	0.88[EUR][1000 genomes]
rs62003661	0.84[EUR][1000 genomes]
rs62005707	0.98[EUR][1000 genomes]
rs62005709	0.99[EUR][1000 genomes]
rs62005710	0.97[EUR][1000 genomes]
rs62005711	0.93[EUR][1000 genomes]
rs71399778	0.99[EUR][1000 genomes]
rs733163	0.82[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs8037531	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9630417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs971755	0.88[EUR][1000 genomes]
rs971756	0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs971757	0.88[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	nsv469619	chr15:74291859-74466321	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv482362	chr15:74291859-74466321	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
rs923118	C15orf39	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74460200-74466400	Enhancers	Spleen	Spleen
2	chr15:74463000-74467400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:74464400-74467600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:74464600-74466800	Enhancers	Fetal Heart	heart
5	chr15:74464600-74467000	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr15:74464600-74467400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:74464600-74467400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:74464600-74467400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr15:74464600-74467400	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr15:74464800-74466600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr15:74464800-74466600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:74464800-74467200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:74464800-74473600	Enhancers	Right Ventricle	heart
14	chr15:74465000-74466600	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr15:74465000-74466800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:74465000-74467200	Enhancers	Lung	lung
17	chr15:74465000-74467400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:74465000-74467400	Enhancers	Osteobl	bone
19	chr15:74465000-74467800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:74465000-74470000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr15:74465200-74466400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr15:74465200-74466600	Enhancers	H1 Cell Line	embryonic stem cell
23	chr15:74465200-74466800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr15:74465200-74467200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:74465200-74467600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:74465200-74469200	Weak transcription	Aorta	Aorta
27	chr15:74465200-74472200	Weak transcription	Brain Substantia Nigra	brain
28	chr15:74465200-74473000	Enhancers	Brain Germinal Matrix	brain
29	chr15:74465400-74466400	Enhancers	Fetal Brain Female	brain
30	chr15:74465400-74466600	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr15:74465400-74467000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr15:74465400-74467200	Enhancers	A549	lung
33	chr15:74465400-74467200	Enhancers	NH-A	brain
34	chr15:74465600-74466400	Enhancers	H9 Cell Line	embryonic stem cell
35	chr15:74465600-74466400	Flanking Active TSS	Ovary	ovary
36	chr15:74465600-74466400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr15:74465600-74466600	Flanking Active TSS	NHDF-Ad	bronchial
38	chr15:74465600-74467200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr15:74465600-74467400	Flanking Active TSS	Fetal Muscle Leg	muscle
40	chr15:74465600-74468000	Enhancers	HSMM	muscle
41	chr15:74465600-74468400	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr15:74465800-74466400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:74465800-74466400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr15:74465800-74466600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr15:74465800-74467000	Enhancers	Fetal Brain Male	brain
46	chr15:74465800-74467200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr15:74465800-74467200	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr15:74465800-74467600	Active TSS	Colonic Mucosa	Colon
49	chr15:74466000-74466400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:74466000-74466600	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine

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