Variant report

Variant	rs2244772
Chromosome Location	chr15:57619702-57619703
allele	C/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	RCOR1	chr15:57619488-57621205	K562	blood:	n/a	n/a
2	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

Variant related genes	Relation type
ENSG00000260870	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11629673	1.00[JPT][hapmap]
rs17819964	1.00[JPT][hapmap]
rs2243451	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247485	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247499	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2247501	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248205	0.84[ASN][1000 genomes]
rs2249219	1.00[JPT][hapmap]
rs2440943	1.00[JPT][hapmap]
rs4238323	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493912	1.00[JPT][hapmap]

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
rs2244772	RSL24D1	cis	parietal	SCAN

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	chr15:57616400-57619800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:57616400-57619800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:57616400-57620400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:57616400-57620400	Weak transcription	Placenta	Placenta
13	chr15:57616800-57621400	Enhancers	Fetal Intestine Large	intestine
14	chr15:57617200-57619800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:57617200-57620000	Enhancers	K562	blood
16	chr15:57617200-57620200	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr15:57617200-57622400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:57617200-57622400	Weak transcription	Hela-S3	cervix
19	chr15:57617600-57624800	Enhancers	Fetal Muscle Leg	muscle
20	chr15:57617600-57625800	Weak transcription	A549	lung
21	chr15:57617800-57622200	Weak transcription	Fetal Thymus	thymus
22	chr15:57618600-57632000	Weak transcription	Spleen	Spleen
23	chr15:57618800-57619800	Enhancers	Muscle Satellite Cultured Cells	--
24	chr15:57619000-57619800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr15:57619000-57623400	Enhancers	HSMM	muscle
26	chr15:57619200-57619800	Enhancers	NH-A	brain
27	chr15:57619200-57619800	Enhancers	Osteobl	bone
28	chr15:57619200-57620000	Enhancers	Stomach Mucosa	stomach
29	chr15:57619200-57621200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:57619200-57621200	Enhancers	NHLF	lung
31	chr15:57619400-57620000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:57619400-57621000	Enhancers	Fetal Lung	lung
33	chr15:57619400-57621000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr15:57619400-57621000	Flanking Active TSS	HSMMtube	muscle
35	chr15:57619400-57621000	Enhancers	NHDF-Ad	bronchial
36	chr15:57619600-57619800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:57619600-57620600	Weak transcription	Psoas Muscle	Psoas
38	chr15:57619600-57620800	Weak transcription	Fetal Muscle Trunk	muscle

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