Variant report

Variant	rs16977401
Chromosome Location	chr15:57619953-57619954
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	PBX3	chr15:57619883-57621128	SK-N-SH	brain:	n/a	chr15:57620240-57620249 chr15:57620836-57620845
2	TCF12	chr15:57619876-57621249	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr15:57619953-57620938	SK-N-SH	brain:	n/a	n/a
4	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
5	JUND	chr15:57619952-57620878	SK-N-SH	brain:	n/a	chr15:57620238-57620247
6	EP300	chr15:57619889-57620914	SK-N-SH	brain:	n/a	n/a
7	RCOR1	chr15:57619488-57621205	K562	blood:	n/a	n/a
8	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
9	EP300	chr15:57619886-57621011	SK-N-SH	brain:	n/a	n/a
10	NFIC	chr15:57619887-57620936	SK-N-SH	brain:	n/a	n/a
11	MAFF	chr15:57619853-57620427	K562	blood:	n/a	n/a
12	PBX3	chr15:57619849-57621138	SK-N-SH	brain:	n/a	chr15:57620240-57620249 chr15:57620836-57620845
13	JUND	chr15:57619938-57620887	SK-N-SH	brain:	n/a	chr15:57620238-57620247
14	EP300	chr15:57619842-57621094	K562	blood:	n/a	chr15:57619853-57619867

Variant related genes	Relation type
ENSG00000260870	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12595188	0.86[EUR][1000 genomes]
rs2243806	0.81[EUR][1000 genomes]
rs2244636	0.93[CEU][hapmap]
rs28691795	0.81[EUR][1000 genomes]
rs28704076	0.81[EUR][1000 genomes]
rs58703516	0.81[EUR][1000 genomes]
rs72736047	0.89[EUR][1000 genomes];0.90[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

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57611400-57620600	Enhancers	Fetal Intestine Small	intestine
2	chr15:57613000-57626800	Weak transcription	Right Atrium	heart
3	chr15:57613000-57635400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:57614600-57621800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr15:57616200-57620000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:57616200-57622200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:57616200-57624600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:57616200-57624800	Weak transcription	Lung	lung
9	chr15:57616400-57620400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:57616400-57620400	Weak transcription	Placenta	Placenta
11	chr15:57616800-57621400	Enhancers	Fetal Intestine Large	intestine
12	chr15:57617200-57620000	Enhancers	K562	blood
13	chr15:57617200-57620200	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr15:57617200-57622400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:57617200-57622400	Weak transcription	Hela-S3	cervix
16	chr15:57617600-57624800	Enhancers	Fetal Muscle Leg	muscle
17	chr15:57617600-57625800	Weak transcription	A549	lung
18	chr15:57617800-57622200	Weak transcription	Fetal Thymus	thymus
19	chr15:57618600-57632000	Weak transcription	Spleen	Spleen
20	chr15:57619000-57623400	Enhancers	HSMM	muscle
21	chr15:57619200-57620000	Enhancers	Stomach Mucosa	stomach
22	chr15:57619200-57621200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:57619200-57621200	Enhancers	NHLF	lung
24	chr15:57619400-57620000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:57619400-57621000	Enhancers	Fetal Lung	lung
26	chr15:57619400-57621000	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr15:57619400-57621000	Flanking Active TSS	HSMMtube	muscle
28	chr15:57619400-57621000	Enhancers	NHDF-Ad	bronchial
29	chr15:57619600-57620600	Weak transcription	Psoas Muscle	Psoas
30	chr15:57619600-57620800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr15:57619800-57620000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:57619800-57620000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:57619800-57620200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr15:57619800-57620200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:57619800-57620200	Flanking Active TSS	NH-A	brain
36	chr15:57619800-57620200	Flanking Active TSS	Osteobl	bone
37	chr15:57619800-57620400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr15:57619800-57620800	Enhancers	Rectal Mucosa Donor 31	rectum

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