Variant report

Variant	rs35565646
Chromosome Location	chr15:40660515-40660516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:386)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:386 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr15:40660442-40660658	K562	blood:	n/a	n/a
2	CHD2	chr15:40660394-40660599	GM12878	blood:	n/a	n/a
3	CTCF	chr15:40660380-40660530	AG09319	gingival:	n/a	n/a
4	RAD21	chr15:40660004-40660751	MCF-7	breast:	n/a	n/a
5	CTCF	chr15:40659934-40660741	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr15:40660380-40660530	HPF	lung:	n/a	n/a
7	CTCF	chr15:40660076-40660616	A549	lung:	n/a	n/a
8	MYC	chr15:40659818-40660700	MCF-7	breast:	n/a	n/a
9	NFIC	chr15:40659864-40660783	ECC-1	luminal epithelium:	n/a	n/a
10	BRCA1	chr15:40660307-40660582	Hela-S3	cervix:	n/a	n/a
11	TEAD4	chr15:40659975-40660652	H1-hESC	embryonic stem cell:	n/a	n/a
12	EGR1	chr15:40660100-40660773	HCT-116	colon:	n/a	n/a
13	YY1	chr15:40660244-40660605	K562	blood:	n/a	n/a
14	CTCF	chr15:40660400-40660550	GM12867	blood:	n/a	n/a
15	CTCF	chr15:40660058-40660594	MCF-7	breast:	n/a	n/a
16	SMC3	chr15:40660366-40660594	HepG2	liver:	n/a	n/a
17	PAX5	chr15:40660174-40660698	GM12892	blood:	n/a	n/a
18	TBL1XR1	chr15:40660408-40660597	GM12878	blood:	n/a	n/a
19	STAT5A	chr15:40660284-40660627	K562	blood:	n/a	n/a
20	CTCF	chr15:40660039-40660637	GM12878	blood:	n/a	n/a
21	CTCF	chr15:40660013-40660546	LNCaP	prostate:	n/a	n/a
22	RAD21	chr15:40659923-40660793	HCT-116	colon:	n/a	n/a
23	CTCF	chr15:40659919-40660783	MCF-7	breast:	n/a	n/a
24	CTCF	chr15:40660460-40660610	A549	lung:	n/a	n/a
25	CEBPB	chr15:40660165-40660627	H1-hESC	embryonic stem cell:	n/a	n/a
26	SETDB1	chr15:40660347-40660736	K562	blood:	n/a	n/a
27	POLR2A	chr15:40659641-40660776	HL-60	blood:	n/a	n/a
28	RAD21	chr15:40659813-40660808	HCT-116	colon:	n/a	n/a
29	CTCF	chr15:40660380-40660530	AG04450	lung:	n/a	n/a
30	RCOR1	chr15:40660219-40660681	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr15:40660400-40660550	GM12864	blood:	n/a	n/a
32	ZBTB7A	chr15:40660358-40660759	K562	blood:	n/a	n/a
33	EGR1	chr15:40660255-40660707	K562	blood:	n/a	n/a
34	CTCF	chr15:40660186-40660604	GM10248	blood:	n/a	n/a
35	MAX	chr15:40660057-40660681	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr15:40660077-40660686	HepG2	liver:	n/a	n/a
37	E2F6	chr15:40660137-40660755	K562	blood:	n/a	n/a
38	CTCF	chr15:40660400-40660550	AG04450	lung:	n/a	n/a
39	RUNX3	chr15:40660259-40660792	GM12878	blood:	n/a	n/a
40	CTCF	chr15:40660380-40660530	SAEC	small airway:	n/a	n/a
41	EP300	chr15:40660030-40660693	H1-hESC	embryonic stem cell:	n/a	n/a
42	RCOR1	chr15:40660361-40660580	GM12878	blood:	n/a	n/a
43	NR2F2	chr15:40660220-40660754	K562	blood:	n/a	n/a
44	MAX	chr15:40659906-40660811	MCF-7	breast:	n/a	n/a
45	TCF3	chr15:40660343-40660586	GM12878	blood:	n/a	n/a
46	YY1	chr15:40659945-40660753	H1-hESC	embryonic stem cell:	n/a	n/a
47	CUX1	chr15:40660396-40660549	K562	blood:	n/a	n/a
48	CTCF	chr15:40660400-40660550	GM12870	blood:	n/a	n/a
49	CEBPB	chr15:40660320-40660605	K562	blood:	n/a	n/a
50	ESRRA	chr15:40659809-40660765	GM12878	blood:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40604227..40604812-chr15:40659800..40660618,2	MCF-7	breast:
2	chr15:40658920..40662804-chr15:40663316..40668232,4	MCF-7	breast:
3	chr15:40659687..40660521-chr2:36824351..36825100,2	Hela-S3	cervix:
4	chr15:40654268..40658108-chr15:40658959..40661427,3	K562	blood:
5	chr15:40654870..40656503-chr15:40658947..40660555,2	MCF-7	breast:
6	chr15:40636446..40637771-chr15:40659706..40660699,14	MCF-7	breast:
7	chr15:40659644..40660927-chr15:40713621..40714773,7	MCF-7	breast:
8	chr15:40636483..40637410-chr15:40659872..40660767,3	K562	blood:
9	chr15:40660065..40660834-chr15:40713817..40714374,2	MCF-7	breast:
10	chr15:40651634..40653250-chr15:40659195..40661061,2	MCF-7	breast:
11	chr15:40659345..40661369-chr15:40727468..40729133,3	K562	blood:
12	chr15:40659883..40661709-chr15:40662718..40664591,2	MCF-7	breast:
13	chr15:40657809..40661993-chr15:40702342..40704983,3	K562	blood:
14	chr15:40659345..40661369-chr15:40727468..40729027,2	K562	blood:
15	chr15:40580563..40582571-chr15:40659855..40662035,2	K562	blood:
16	chr15:40631758..40634462-chr15:40659942..40662520,2	MCF-7	breast:
17	chr15:40660096..40660848-chr15:40733304..40733861,2	MCF-7	breast:
18	chr15:40592964..40595211-chr15:40658424..40661037,2	MCF-7	breast:
19	chr15:40574173..40574897-chr15:40659842..40660788,3	MCF-7	breast:
20	chr15:40660049..40660758-chr15:40762439..40763200,2	MCF-7	breast:
21	chr15:40659428..40662346-chr15:40732080..40734388,2	MCF-7	breast:

No data

Variant related genes	Relation type
LINC00594	TF binding region
DISP2	TF binding region
ENSG00000188549	Chromatin interaction
ENSG00000169105	Chromatin interaction
ENSG00000259714	Chromatin interaction
ENSG00000137841	Chromatin interaction
ENSG00000140320	Chromatin interaction
ENSG00000261374	Chromatin interaction
ENSG00000128928	Chromatin interaction
ENSG00000140323	Chromatin interaction
ENSG00000230778	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11634187	0.89[EUR][1000 genomes]
rs11636147	0.89[EUR][1000 genomes]
rs12905240	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12913300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16970633	0.88[EUR][1000 genomes]
rs2289328	0.92[EUR][1000 genomes]
rs35777573	0.89[EUR][1000 genomes]
rs3803359	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803360	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56221586	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71472433	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7164581	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7164606	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs35565646	RP11-64K12.4	cis	Nerve Tibial	GTEx
rs35565646	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs35565646	RP11-64K12.4	cis	Skin Sun Exposed Lower leg	GTEx
rs35565646	DISP2	cis	Esophagus Mucosa	GTEx
rs35565646	RP11-64K12.4	cis	Esophagus Mucosa	GTEx
rs35565646	RP11-64K12.4	cis	Adipose Subcutaneous	GTEx
rs35565646	DISP2	cis	Nerve Tibial	GTEx
rs35565646	DISP2	cis	Esophagus Muscularis	GTEx
rs35565646	DISP2	cis	Adipose Subcutaneous	GTEx
rs35565646	DISP2	cis	Muscle Skeletal	GTEx
rs35565646	DISP2	cis	Skin Sun Exposed Lower leg	GTEx
rs35565646	DISP2	cis	lung	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40656200-40661000	Enhancers	Fetal Heart	heart
2	chr15:40657400-40661200	Enhancers	Fetal Brain Male	brain
3	chr15:40658400-40660600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr15:40659000-40660800	Enhancers	Stomach Mucosa	stomach
5	chr15:40659000-40661000	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr15:40659200-40660800	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr15:40659400-40660800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr15:40659400-40660800	Flanking Active TSS	Dnd41	blood
9	chr15:40659400-40660800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr15:40659400-40661000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr15:40659400-40661000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr15:40659400-40661000	Enhancers	HMEC	breast
13	chr15:40659400-40661400	Enhancers	Lung	lung
14	chr15:40659600-40660600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:40659600-40660600	Flanking Active TSS	Right Ventricle	heart
16	chr15:40659600-40660800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:40659600-40660800	Flanking Active TSS	Colonic Mucosa	Colon
18	chr15:40659600-40660800	Enhancers	Fetal Intestine Large	intestine
19	chr15:40659600-40660800	Flanking Active TSS	Spleen	Spleen
20	chr15:40659800-40660600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr15:40659800-40660600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:40659800-40660600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr15:40659800-40660600	Active TSS	Osteobl	bone
24	chr15:40659800-40660800	Flanking Active TSS	Brain Cingulate Gyrus	brain
25	chr15:40659800-40660800	Enhancers	Placenta	Placenta
26	chr15:40659800-40660800	Bivalent/Poised TSS	HepG2	liver
27	chr15:40659800-40661000	Enhancers	Fetal Lung	lung
28	chr15:40659800-40661000	Enhancers	NHDF-Ad	bronchial
29	chr15:40660000-40660600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr15:40660000-40660600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:40660000-40660600	Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr15:40660000-40660600	Active TSS	Colon Smooth Muscle	Colon
33	chr15:40660000-40660600	Active TSS	Rectal Smooth Muscle	rectum
34	chr15:40660000-40660600	Active TSS	HSMM	muscle
35	chr15:40660000-40660800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:40660000-40660800	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:40660000-40660800	Flanking Active TSS	Brain Germinal Matrix	brain
38	chr15:40660200-40660600	Enhancers	Primary T cells fromperipheralblood	blood
39	chr15:40660200-40660600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:40660200-40660600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr15:40660200-40660600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:40660200-40660600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:40660200-40660600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:40660200-40660600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:40660200-40660600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:40660200-40660600	Active TSS	Brain Angular Gyrus	brain
47	chr15:40660200-40660600	Active TSS	Brain Anterior Caudate	brain
48	chr15:40660200-40660600	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr15:40660200-40660600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:40660200-40660600	Active TSS	Brain Substantia Nigra	brain

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