Variant report

Variant	rs35842610
Chromosome Location	chr15:40882316-40882317
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	CTCF	chr15:40881958-40882333	A549	lung:	n/a	chr15:40882149-40882167 chr15:40882150-40882166 chr15:40882152-40882165 chr15:40882151-40882172
2	MXI1	chr15:40882064-40882363	GM12878	blood:	n/a	n/a
3	RAD21	chr15:40881896-40882490	HCT-116	colon:	n/a	chr15:40882150-40882169
4	ZNF143	chr15:40881975-40882333	GM12878	blood:	n/a	n/a
5	CTCF	chr15:40881931-40882347	K562	blood:	n/a	chr15:40882149-40882167 chr15:40882150-40882166 chr15:40882152-40882165 chr15:40882151-40882172
6	RAD21	chr15:40881919-40882406	ECC-1	luminal epithelium:	n/a	chr15:40882150-40882169
7	NFIC	chr15:40881916-40882391	GM12878	blood:	n/a	n/a
8	RUNX3	chr15:40881949-40882550	GM12878	blood:	n/a	n/a
9	SMC3	chr15:40881997-40882391	GM12878	blood:	n/a	chr15:40882151-40882165
10	CTCF	chr15:40881903-40882392	A549	lung:	n/a	chr15:40882149-40882167 chr15:40882150-40882166 chr15:40882152-40882165 chr15:40882151-40882172
11	RAD21	chr15:40881824-40882713	SK-N-SH	brain:	n/a	chr15:40882150-40882169
12	MAX	chr15:40882039-40882331	GM12878	blood:	n/a	n/a
13	TBL1XR1	chr15:40882064-40882349	K562	blood:	n/a	n/a
14	TBL1XR1	chr15:40882029-40882538	K562	blood:	n/a	n/a
15	CTCF	chr15:40882309-40882398	GM19238	blood:	n/a	n/a
16	CTCF	chr15:40881954-40882418	K562	blood:	n/a	chr15:40882149-40882167 chr15:40882150-40882166 chr15:40882152-40882165 chr15:40882151-40882172
17	CTCF	chr15:40882312-40882409	A549	lung:	n/a	n/a
18	RAD21	chr15:40881958-40882353	Hela-S3	cervix:	n/a	chr15:40882150-40882169
19	CTCF	chr15:40881949-40882349	IMR90	lung:	n/a	chr15:40882149-40882167 chr15:40882150-40882166 chr15:40882152-40882165 chr15:40882151-40882172
20	MAX	chr15:40881984-40882638	K562	blood:	n/a	n/a
21	PAX5	chr15:40882113-40882472	GM12891	blood:	n/a	n/a
22	SMC3	chr15:40881936-40882348	Hela-S3	cervix:	n/a	chr15:40882151-40882165
23	MYC	chr15:40881984-40882658	K562	blood:	n/a	n/a
24	SMC3	chr15:40881972-40882320	HepG2	liver:	n/a	chr15:40882151-40882165
25	CTCF	chr15:40881958-40882357	K562	blood:	n/a	chr15:40882149-40882167 chr15:40882150-40882166 chr15:40882152-40882165 chr15:40882151-40882172
26	CTCF	chr15:40881977-40882402	MCF-7	breast:	n/a	chr15:40882149-40882167 chr15:40882150-40882166 chr15:40882152-40882165 chr15:40882151-40882172
27	RAD21	chr15:40881911-40882479	HCT-116	colon:	n/a	chr15:40882150-40882169
28	PAX5	chr15:40882028-40882516	GM12878	blood:	n/a	n/a
29	RAD21	chr15:40881982-40882416	MCF-7	breast:	n/a	chr15:40882150-40882169
30	BCLAF1	chr15:40881933-40882454	GM12878	blood:	n/a	n/a
31	RAD21	chr15:40881979-40882393	ECC-1	luminal epithelium:	n/a	chr15:40882150-40882169
32	RAD21	chr15:40881880-40882400	MCF-7	breast:	n/a	chr15:40882150-40882169
33	RAD21	chr15:40881904-40882377	A549	lung:	n/a	chr15:40882150-40882169
34	CTCF	chr15:40882300-40882394	MCF-7	breast:	n/a	n/a
35	RAD21	chr15:40881970-40882391	HepG2	liver:	n/a	chr15:40882150-40882169
36	RCOR1	chr15:40881777-40882336	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr15:40881848-40882439	HCT-116	colon:	n/a	chr15:40882149-40882167 chr15:40882150-40882166 chr15:40882152-40882165 chr15:40882151-40882172
38	GTF3C2	chr15:40881970-40883215	K562	blood:	n/a	n/a
39	CTCF	chr15:40882281-40882382	GM12892	blood:	n/a	n/a
40	RAD21	chr15:40881984-40882346	IMR90	lung:	n/a	chr15:40882150-40882169
41	BHLHE40	chr15:40881979-40882337	GM12878	blood:	n/a	n/a
42	CTCF	chr15:40881986-40882318	HepG2	liver:	n/a	chr15:40882149-40882167 chr15:40882150-40882166 chr15:40882152-40882165 chr15:40882151-40882172
43	CTCF	chr15:40882311-40882397	MCF-7	breast:	n/a	n/a
44	GATA2	chr15:40881880-40882331	SH-SY5Y	brain:	n/a	chr15:40882173-40882183
45	PAX5	chr15:40882208-40882449	GM12892	blood:	n/a	n/a
46	ZNF384	chr15:40881930-40882503	GM12878	blood:	n/a	n/a
47	PAX5	chr15:40882044-40882464	GM12878	blood:	n/a	n/a
48	RUNX3	chr15:40881854-40882587	GM12878	blood:	n/a	n/a
49	RAD21	chr15:40881961-40882332	H1-hESC	embryonic stem cell:	n/a	chr15:40882150-40882169
50	ZNF143	chr15:40881953-40882339	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40875697..40878218-chr15:40879677..40882700,3	K562	blood:
2	chr15:40876093..40878968-chr15:40880473..40883736,4	K562	blood:
3	chr15:40761695..40764555-chr15:40881844..40883742,2	K562	blood:
4	chr15:40870931..40871614-chr15:40881583..40882320,2	K562	blood:
5	chr15:40845102..40847771-chr15:40879538..40882866,3	K562	blood:
6	chr15:40867638..40870164-chr15:40881425..40883040,2	K562	blood:

Variant related genes	Relation type
CASC5	TF binding region
ENSG00000169105	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10152546	0.93[EUR][1000 genomes]
rs1044474	0.90[EUR][1000 genomes]
rs10518697	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1058734	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11070283	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11630273	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11633184	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11637245	0.92[EUR][1000 genomes]
rs11637422	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12324748	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12385982	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12441754	0.85[EUR][1000 genomes]
rs12903817	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12907442	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12908316	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12913296	0.93[EUR][1000 genomes]
rs12913739	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915171	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12915636	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13329076	0.87[EUR][1000 genomes]
rs17673703	0.93[EUR][1000 genomes]
rs17674454	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17747423	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17747633	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1814541	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1814542	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2412525	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28529389	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28634695	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28647196	0.84[EUR][1000 genomes]
rs28669075	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34739056	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34824658	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35127391	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35684277	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4923880	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4924486	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62019876	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62019879	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71471880	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7165509	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7170288	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7175747	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8029530	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8036891	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8037180	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8038122	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8042386	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9920642	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9920676	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs35842610	C15orf57	cis	Nerve Tibial	GTEx
rs35842610	C15orf57	cis	Artery Aorta	GTEx
rs35842610	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs35842610	C15orf57	cis	lung	GTEx
rs35842610	C15orf57	cis	Muscle Skeletal	GTEx
rs35842610	C15orf57	cis	Esophagus Muscularis	GTEx
rs35842610	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs35842610	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs35842610	C15orf57	cis	Artery Tibial	GTEx
rs35842610	C15orf57	cis	Stomach	GTEx
rs35842610	CCDC32	cis	multi-tissue	Pritchard
rs35842610	RP11-111A22.1	cis	Artery Aorta	GTEx
rs35842610	RP11-111A22.1	cis	Artery Tibial	GTEx
rs35842610	RAD51	cis	multi-tissue	Pritchard
rs35842610	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs35842610	C15orf57	cis	Heart Left Ventricle	GTEx
rs35842610	C15orf57	cis	Adipose Subcutaneous	GTEx
rs35842610	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs35842610	RP11-111A22.1	cis	lung	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40867400-40883600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr15:40881600-40882400	Active TSS	Brain Anterior Caudate	brain
3	chr15:40881600-40882400	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr15:40881600-40882600	Active TSS	Brain Angular Gyrus	brain
5	chr15:40881800-40882400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr15:40881800-40882400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:40881800-40882400	Active TSS	Brain Cingulate Gyrus	brain
8	chr15:40881800-40882400	Active TSS	Fetal Heart	heart
9	chr15:40881800-40882400	Enhancers	HMEC	breast
10	chr15:40881800-40882600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:40881800-40882600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:40881800-40882600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:40881800-40882600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:40881800-40882600	Active TSS	A549	lung
15	chr15:40881800-40882600	Active TSS	NHDF-Ad	bronchial
16	chr15:40881800-40882600	Active TSS	NHLF	lung
17	chr15:40881800-40882800	Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr15:40881800-40882800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr15:40881800-40882800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:40881800-40882800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:40881800-40882800	Flanking Active TSS	Dnd41	blood
22	chr15:40881800-40883000	Active TSS	Osteobl	bone
23	chr15:40881800-40883200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:40881800-40883200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:40881800-40883200	Enhancers	Primary B cells from peripheral blood	blood
26	chr15:40882000-40882400	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr15:40882000-40882400	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr15:40882000-40882400	Active TSS	Primary T cells from cord blood	blood
29	chr15:40882000-40882400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:40882000-40882400	Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr15:40882000-40882400	Active TSS	Colon Smooth Muscle	Colon
32	chr15:40882000-40882400	Active TSS	Placenta	Placenta
33	chr15:40882000-40882600	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr15:40882000-40882600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr15:40882000-40882600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr15:40882000-40882600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr15:40882000-40882600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr15:40882000-40882600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr15:40882000-40882600	Active TSS	Fetal Brain Female	brain
40	chr15:40882000-40882600	Active TSS	Rectal Smooth Muscle	rectum
41	chr15:40882000-40882600	Active TSS	GM12878-XiMat	blood
42	chr15:40882000-40882600	Active TSS	Hela-S3	cervix
43	chr15:40882000-40882600	Active TSS	K562	blood
44	chr15:40882000-40882800	Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr15:40882000-40883000	Active TSS	Fetal Kidney	kidney
46	chr15:40882000-40883200	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr15:40882000-40883200	Active TSS	Ovary	ovary
48	chr15:40882000-40886200	Weak transcription	Lung	lung
49	chr15:40882200-40882400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr15:40882200-40882400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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