Variant report

Variant	rs9630417
Chromosome Location	chr15:74464183-74464184
allele	A/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	POLR2A	chr15:74460105-74471859	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74462656..74465271-chr15:74469340..74471274,2	K562	blood:

Variant related genes	Relation type
ISLR	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11630317	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs11630924	0.86[EUR][1000 genomes]
rs11631509	0.83[EUR][1000 genomes]
rs11631944	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.96[EUR][1000 genomes]
rs11639090	0.98[EUR][1000 genomes]
rs11639369	1.00[CHD][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs11854957	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs11855667	0.83[EUR][1000 genomes]
rs11857410	1.00[CHD][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs12899173	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs12907503	0.93[EUR][1000 genomes]
rs12911581	0.82[EUR][1000 genomes]
rs12912258	0.82[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs12912578	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.97[EUR][1000 genomes]
rs12913041	0.97[EUR][1000 genomes]
rs12915891	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs13259	0.91[CEU][hapmap];0.98[EUR][1000 genomes]
rs2062309	0.88[AMR][1000 genomes];0.95[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];0.98[EUR][1000 genomes]
rs34147822	0.86[EUR][1000 genomes]
rs34573746	0.85[EUR][1000 genomes]
rs34868798	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs351242	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs35255788	0.86[EUR][1000 genomes]
rs35462746	0.99[EUR][1000 genomes]
rs35661273	0.98[EUR][1000 genomes]
rs3848160	0.98[EUR][1000 genomes]
rs3848161	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.98[EUR][1000 genomes]
rs3888004	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.98[EUR][1000 genomes]
rs409856	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs5742915	1.00[CHD][hapmap]
rs62003660	0.86[EUR][1000 genomes]
rs62003661	0.83[EUR][1000 genomes]
rs62005707	0.98[EUR][1000 genomes]
rs62005709	0.98[EUR][1000 genomes]
rs62005710	0.96[EUR][1000 genomes]
rs62005711	0.91[EUR][1000 genomes]
rs71399778	0.98[EUR][1000 genomes]
rs733163	0.82[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs8037531	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs923118	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	0.86[EUR][1000 genomes]
rs971756	0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs971757	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758387	chr15:74215114-74464916	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv2760040	chr15:74215114-74464916	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv428308	chr15:74215114-74464916	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
rs9630417	C15orf39	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74449400-74465600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:74460000-74465600	Enhancers	Fetal Muscle Leg	muscle
3	chr15:74460200-74465600	Enhancers	Ovary	ovary
4	chr15:74460200-74466000	Enhancers	Fetal Muscle Trunk	muscle
5	chr15:74460200-74466000	Enhancers	Fetal Stomach	stomach
6	chr15:74460200-74466400	Enhancers	Spleen	Spleen
7	chr15:74460600-74464600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:74461000-74465600	Enhancers	Fetal Lung	lung
9	chr15:74461000-74465600	Enhancers	Placenta	Placenta
10	chr15:74461400-74464800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:74461400-74465000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:74461400-74465200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:74461600-74464800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:74461600-74465200	Weak transcription	HSMMtube	muscle
15	chr15:74461600-74466200	Weak transcription	Pancreas	Pancrea
16	chr15:74462000-74464400	Weak transcription	Adipose Nuclei	Adipose
17	chr15:74462000-74464400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:74462000-74464400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr15:74462200-74464800	Weak transcription	Left Ventricle	heart
20	chr15:74462600-74464400	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:74462600-74464600	Weak transcription	Fetal Heart	heart
22	chr15:74462800-74464800	Weak transcription	Fetal Brain Male	brain
23	chr15:74463000-74467400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:74463200-74464400	Weak transcription	Fetal Kidney	kidney
25	chr15:74463200-74464400	Weak transcription	GM12878-XiMat	blood
26	chr15:74463200-74464600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:74463400-74464400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:74463400-74464600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:74463800-74464200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr15:74463800-74464800	Weak transcription	Right Ventricle	heart
31	chr15:74463800-74465000	Weak transcription	Lung	lung
32	chr15:74463800-74465200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr15:74464000-74464400	Weak transcription	Right Atrium	heart
34	chr15:74464000-74465000	Weak transcription	Colonic Mucosa	Colon

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