Variant report

Variant	rs11638662
Chromosome Location	chr15:40546674-40546675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:40546659-40546777	MCF-7	breast:	n/a	n/a
2	CTCF	chr15:40546624-40546799	K562	blood:	n/a	n/a
3	CTCF	chr15:40546673-40546789	GM12878	blood:	n/a	n/a
4	CTCF	chr15:40546600-40546750	SK-N-SH_RA	brain:	n/a	n/a
5	CTCF	chr15:40546640-40546790	SK-N-SH_RA	brain:	n/a	n/a
6	CTCF	chr15:40546663-40546775	GM19239	blood:	n/a	n/a
7	CTCF	chr15:40546640-40546790	BE2_C	brain:	n/a	n/a
8	CTCF	chr15:40546666-40546778	MCF-7	breast:	n/a	n/a
9	CTCF	chr15:40546640-40546826	K562	blood:	n/a	n/a
10	CTCF	chr15:40546631-40546778	NHEK	skin:	n/a	n/a
11	CTCF	chr15:40546648-40546803	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr15:40546640-40546790	HMEC	breast:	n/a	n/a
13	CTCF	chr15:40546560-40546710	HPAF	blood vessel:	n/a	n/a
14	CTCF	chr15:40546580-40546730	GM12864	blood:	n/a	n/a
15	CTCF	chr15:40546600-40546750	HBMEC	blood vessel:	n/a	n/a
16	CTCF	chr15:40546660-40546810	GM12864	blood:	n/a	n/a
17	CTCF	chr15:40546660-40546810	HAc	cerebellar:	n/a	n/a
18	CTCF	chr15:40546620-40546770	MCF-7	breast:	n/a	n/a
19	CTCF	chr15:40546602-40546784	GM12878	blood:	n/a	n/a
20	CTCF	chr15:40546620-40546770	GM12873	blood:	n/a	n/a
21	CTCF	chr15:40546620-40546770	Hela-S3	cervix:	n/a	n/a
22	CTCF	chr15:40546660-40546810	GM12866	blood:	n/a	n/a
23	CTCF	chr15:40546647-40546792	GM12892	blood:	n/a	n/a
24	RAD21	chr15:40546643-40546790	H1-hESC	embryonic stem cell:	n/a	chr15:40546711-40546721 chr15:40546709-40546721
25	CTCF	chr15:40546641-40546796	GM19238	blood:	n/a	n/a
26	CTCF	chr15:40546580-40546730	HRE	kidney:	n/a	n/a
27	CTCF	chr15:40546660-40546810	GM12873	blood:	n/a	n/a
28	CTCF	chr15:40546669-40546771	MCF-7	breast:	n/a	n/a
29	CTCF	chr15:40546640-40546790	WERI-Rb-1	eye:	n/a	n/a
30	CTCF	chr15:40546640-40546790	HepG2	liver:	n/a	n/a
31	CTCF	chr15:40546643-40546803	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr15:40546620-40546770	HEK293	kidney:	n/a	n/a
33	CTCF	chr15:40546620-40546770	HMF	breast:	n/a	n/a
34	CTCF	chr15:40546665-40546771	GM19240	blood:	n/a	n/a
35	CTCF	chr15:40546560-40546710	HUVEC	blood vessel:	n/a	n/a
36	CTCF	chr15:40546655-40546781	GM12891	blood:	n/a	n/a
37	CTCF	chr15:40546660-40546810	HMF	breast:	n/a	n/a
38	CTCF	chr15:40546674-40546781	MCF-7	breast:	n/a	n/a
39	CTCF	chr15:40546640-40546790	GM06990	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40529010..40532751-chr15:40545483..40549200,3	MCF-7	breast:
2	chr15:40546251..40550526-chr15:40556944..40560237,5	K562	blood:
3	chr15:40367965..40369899-chr15:40546441..40549267,2	K562	blood:
4	chr15:40508399..40512238-chr15:40546520..40549744,3	MCF-7	breast:

No data

Variant related genes	Relation type
C15orf56	TF binding region
ENSG00000137843	Chromatin interaction
ENSG00000156970	Chromatin interaction
ENSG00000259288	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1048163	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048164	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11634057	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634409	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11636097	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636147	1.00[JPT][hapmap]
rs11638733	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12050520	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17733008	1.00[JPT][hapmap]
rs2018127	1.00[JPT][hapmap]
rs2289327	1.00[JPT][hapmap]
rs55799438	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55863440	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55974545	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731469	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731470	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040419	1.00[JPT][hapmap]
rs900054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv904095	chr15:40525430-40591570	Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv471240	chr15:40528155-40595627	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11638662	RPAP1	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40545200-40547600	Strong transcription	HMEC	breast
2	chr15:40545800-40549600	Strong transcription	NHEK	skin
3	chr15:40546000-40547400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:40546000-40547800	Enhancers	Pancreas	Pancrea
5	chr15:40546000-40548000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:40546000-40549200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:40546000-40550600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:40546000-40558400	Weak transcription	Brain Anterior Caudate	brain
9	chr15:40546000-40558600	Weak transcription	Brain Angular Gyrus	brain
10	chr15:40546000-40571800	Weak transcription	Right Ventricle	heart
11	chr15:40546200-40546800	Bivalent Enhancer	Fetal Intestine Small	intestine
12	chr15:40546200-40547000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:40546200-40547800	Weak transcription	Gastric	stomach
14	chr15:40546200-40548400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:40546200-40549800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:40546200-40551600	Enhancers	Placenta	Placenta
17	chr15:40546200-40552600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr15:40546200-40568200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr15:40546400-40547600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:40546400-40551200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr15:40546600-40547000	Weak transcription	Esophagus	oesophagus
22	chr15:40546600-40547600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
23	chr15:40546600-40547600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr15:40546600-40548600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:40546600-40550800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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