Variant report

Variant	rs4534776
Chromosome Location	chr15:57620776-57620777
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	MYC	chr15:57620329-57621031	K562	blood:	n/a	n/a
2	MAX	chr15:57620496-57620982	K562	blood:	n/a	n/a
3	RAD21	chr15:57620680-57621088	SK-N-SH_RA	brain:	n/a	n/a
4	TEAD4	chr15:57620172-57621131	K562	blood:	n/a	n/a
5	PBX3	chr15:57619883-57621128	SK-N-SH	brain:	n/a	chr15:57620240-57620249 chr15:57620836-57620845
6	POLR2A	chr15:57619998-57620966	IMR90	lung:	n/a	n/a
7	TBP	chr15:57620388-57620892	K562	blood:	n/a	n/a
8	MAZ	chr15:57620392-57621295	K562	blood:	n/a	n/a
9	RXRA	chr15:57619969-57620793	SK-N-SH	brain:	n/a	n/a
10	ESR1	chr15:57620232-57620803	T-47D	breast:	n/a	chr15:57620535-57620550
11	MAFF	chr15:57620639-57621018	K562	blood:	n/a	n/a
12	TCF12	chr15:57619876-57621249	SK-N-SH	brain:	n/a	n/a
13	CTCF	chr15:57620740-57621090	H1-hESC	embryonic stem cell:	n/a	n/a
14	ATF1	chr15:57620393-57621062	K562	blood:	n/a	n/a
15	RAD21	chr15:57620688-57621173	H1-hESC	embryonic stem cell:	n/a	n/a
16	BHLHE40	chr15:57620376-57621177	K562	blood:	n/a	n/a
17	TAF1	chr15:57620141-57620804	SK-N-SH	brain:	n/a	n/a
18	SIN3AK20	chr15:57620131-57620826	SK-N-SH	brain:	n/a	n/a
19	EP300	chr15:57619965-57621212	SK-N-SH	brain:	n/a	n/a
20	RXRA	chr15:57620061-57620830	SK-N-SH	brain:	n/a	n/a
21	TCF12	chr15:57619953-57620938	SK-N-SH	brain:	n/a	n/a
22	GATA3	chr15:57619854-57621201	SK-N-SH	brain:	n/a	chr15:57619860-57619870 chr15:57620366-57620375 chr15:57619862-57619872 chr15:57619856-57619877 chr15:57619863-57619870
23	MEF2A	chr15:57620011-57620846	SK-N-SH	brain:	n/a	chr15:57620775-57620790
24	JUND	chr15:57620000-57621106	SK-N-SH	brain:	n/a	chr15:57620238-57620247
25	TBL1XR1	chr15:57620695-57621034	K562	blood:	n/a	n/a
26	JUND	chr15:57619952-57620878	SK-N-SH	brain:	n/a	chr15:57620238-57620247
27	POLR2A	chr15:57620040-57620894	U87	brain:	n/a	n/a
28	FOSL2	chr15:57620039-57620814	SK-N-SH	brain:	n/a	chr15:57620238-57620247
29	POLR2A	chr15:57620563-57620832	K562	blood:	n/a	n/a
30	RAD21	chr15:57620669-57621035	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr15:57620708-57621118	K562	blood:	n/a	n/a
32	EP300	chr15:57619889-57620914	SK-N-SH	brain:	n/a	n/a
33	HCFC1	chr15:57620625-57621149	K562	blood:	n/a	n/a
34	TEAD4	chr15:57620005-57620854	SK-N-SH	brain:	n/a	n/a
35	RCOR1	chr15:57619488-57621205	K562	blood:	n/a	n/a
36	GATA3	chr15:57619138-57621233	SK-N-SH	brain:	n/a	chr15:57619860-57619870 chr15:57620366-57620375 chr15:57619862-57619872 chr15:57619856-57619877 chr15:57619863-57619870
37	ARID3A	chr15:57620248-57621103	K562	blood:	n/a	n/a
38	CTCF	chr15:57620740-57621010	BE2_C	brain:	n/a	n/a
39	EP300	chr15:57619886-57621011	SK-N-SH	brain:	n/a	n/a
40	RAD21	chr15:57620771-57621024	SK-N-SH_RA	brain:	n/a	n/a
41	JUND	chr15:57620280-57621123	K562	blood:	n/a	n/a
42	YY1	chr15:57620190-57620807	SK-N-SH	brain:	n/a	n/a
43	STAT3	chr15:57620714-57620818	MCF10A-Er-Src	breast:	n/a	n/a
44	NFIC	chr15:57619887-57620936	SK-N-SH	brain:	n/a	n/a
45	CUX1	chr15:57619998-57621043	K562	blood:	n/a	n/a
46	RAD21	chr15:57620739-57621106	H1-hESC	embryonic stem cell:	n/a	n/a
47	MAFK	chr15:57620111-57621009	K562	blood:	n/a	chr15:57620232-57620247 chr15:57620369-57620378 chr15:57620368-57620378 chr15:57620233-57620244
48	CTCF	chr15:57620700-57620850	HFF-Myc	foreskin:	n/a	n/a
49	TBL1XR1	chr15:57620638-57620829	K562	blood:	n/a	n/a
50	FOSL2	chr15:57619985-57620966	SK-N-SH	brain:	n/a	chr15:57620238-57620247

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57600919..57606103-chr15:57620754..57624822,5	K562	blood:

Variant related genes	Relation type
ENSG00000260870	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1007048	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10459625	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11071311	0.85[JPT][hapmap]
rs11631073	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11857206	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12906829	0.88[ASN][1000 genomes]
rs12917506	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17820184	0.85[JPT][hapmap]
rs2414501	0.81[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs4774256	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4774924	0.85[JPT][hapmap]
rs4774926	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs4774927	0.85[JPT][hapmap]
rs4774933	0.84[EUR][1000 genomes]
rs61999616	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61999617	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs749248	0.88[EUR][1000 genomes];0.98[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	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4534776	RSL24D1	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57613000-57626800	Weak transcription	Right Atrium	heart
2	chr15:57613000-57635400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:57614600-57621800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:57616200-57622200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:57616200-57624600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:57616200-57624800	Weak transcription	Lung	lung
7	chr15:57616800-57621400	Enhancers	Fetal Intestine Large	intestine
8	chr15:57617200-57622400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:57617200-57622400	Weak transcription	Hela-S3	cervix
10	chr15:57617600-57624800	Enhancers	Fetal Muscle Leg	muscle
11	chr15:57617600-57625800	Weak transcription	A549	lung
12	chr15:57617800-57622200	Weak transcription	Fetal Thymus	thymus
13	chr15:57618600-57632000	Weak transcription	Spleen	Spleen
14	chr15:57619000-57623400	Enhancers	HSMM	muscle
15	chr15:57619200-57621200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:57619200-57621200	Enhancers	NHLF	lung
17	chr15:57619400-57621000	Enhancers	Fetal Lung	lung
18	chr15:57619400-57621000	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr15:57619400-57621000	Flanking Active TSS	HSMMtube	muscle
20	chr15:57619400-57621000	Enhancers	NHDF-Ad	bronchial
21	chr15:57619600-57620800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr15:57619800-57620800	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr15:57620000-57620800	Flanking Active TSS	K562	blood
24	chr15:57620000-57621000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:57620000-57621200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:57620200-57620800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:57620400-57620800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:57620400-57620800	Enhancers	Placenta	Placenta
29	chr15:57620600-57620800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:57620600-57620800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:57620600-57620800	Flanking Active TSS	NH-A	brain
32	chr15:57620600-57620800	Flanking Active TSS	Osteobl	bone
33	chr15:57620600-57621000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:57620600-57621000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr15:57620600-57621200	Enhancers	Psoas Muscle	Psoas
36	chr15:57620600-57626200	Weak transcription	Fetal Intestine Small	intestine

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