Variant report

Variant	rs10412762
Chromosome Location	chr19:38653613-38653614
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr19:38653576-38653628	Hela-S3	cervix:	n/a	n/a
2	ELF1	chr19:38653318-38653642	GM12878	blood:	n/a	n/a
3	CBX3	chr19:38653116-38653769	K562	blood:	n/a	n/a
4	MAX	chr19:38653263-38653677	K562	blood:	n/a	n/a
5	ZNF143	chr19:38653408-38653730	H1-hESC	embryonic stem cell:	n/a	n/a
6	HCFC1	chr19:38653436-38653681	K562	blood:	n/a	n/a
7	TRIM28	chr19:38653206-38653747	K562	blood:	n/a	n/a
8	USF1	chr19:38653265-38653776	A549	lung:	n/a	n/a
9	USF1	chr19:38653329-38653646	H1-hESC	embryonic stem cell:	n/a	n/a
10	CBX3	chr19:38653204-38653747	K562	blood:	n/a	n/a
11	USF1	chr19:38653285-38653659	K562	blood:	n/a	n/a
12	USF1	chr19:38653346-38653674	ECC-1	luminal epithelium:	n/a	n/a
13	USF1	chr19:38653508-38653622	HepG2	liver:	n/a	n/a
14	ZNF143	chr19:38653480-38653625	GM12878	blood:	n/a	n/a
15	ZNF143	chr19:38653377-38653668	K562	blood:	n/a	n/a
16	SIX5	chr19:38653501-38653687	GM12878	blood:	n/a	n/a
17	KAP1	chr19:38653189-38653798	K562	blood:	n/a	n/a
18	USF1	chr19:38653314-38653675	H1-hESC	embryonic stem cell:	n/a	n/a
19	SETDB1	chr19:38653245-38653678	U2OS	brain:	n/a	n/a
20	USF1	chr19:38653047-38653837	A549	lung:	n/a	n/a
21	USF1	chr19:38653160-38653757	A549	lung:	n/a	n/a
22	TCF12	chr19:38652871-38653998	A549	lung:	n/a	n/a
23	CTCF	chr19:38653520-38653670	A549	lung:	n/a	n/a

No data

Variant related genes	Relation type
SIPA1L3	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10401165	0.89[ASN][1000 genomes]
rs10403716	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412865	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10413751	0.81[JPT][hapmap]
rs10420506	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10422665	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1614979	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs1654349	0.81[JPT][hapmap]
rs1654365	0.87[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs1725475	0.81[JPT][hapmap]
rs1725512	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs2005054	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2010234	0.84[YRI][hapmap]
rs2082442	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2082443	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28495744	0.85[ASN][1000 genomes]
rs28581256	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4802233	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs4802247	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4802256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802278	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs4803786	0.93[ASN][1000 genomes]
rs4803800	0.82[EUR][1000 genomes]
rs4803801	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4803802	0.82[EUR][1000 genomes]
rs4803803	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4803809	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803810	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803828	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803829	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803862	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs56166457	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59185302	0.93[ASN][1000 genomes]
rs59579475	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59924887	0.93[ASN][1000 genomes]
rs61388128	0.93[ASN][1000 genomes]
rs6508767	0.89[ASN][1000 genomes]
rs71179415	0.82[ASN][1000 genomes]
rs7245788	0.93[ASN][1000 genomes]
rs7248428	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7250034	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256332	0.85[ASN][1000 genomes]
rs73627654	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73627663	0.93[ASN][1000 genomes]
rs73627676	0.93[ASN][1000 genomes]
rs73627686	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73930553	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs754123	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8105468	0.93[ASN][1000 genomes]
rs855601	0.81[JPT][hapmap]
rs855603	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs855633	0.88[CEU][hapmap];0.91[CHB][hapmap]
rs855636	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs855637	0.81[JPT][hapmap]
rs860623	0.94[CEU][hapmap];0.90[CHB][hapmap]
rs863020	0.94[CEU][hapmap];0.90[CHB][hapmap]
rs941039	0.94[CEU][hapmap];0.90[CHB][hapmap]
rs941040	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs9941456	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10412762	SIPA1L3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38638200-38667200	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr19:38643800-38654800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr19:38644000-38659200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:38645600-38660800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:38646000-38661000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr19:38650800-38653800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
7	chr19:38651200-38653800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:38651200-38654000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:38651400-38653800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
10	chr19:38651400-38658400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:38652000-38653800	ZNF genes & repeats	Fetal Intestine Small	intestine
12	chr19:38652000-38654000	ZNF genes & repeats	Fetal Stomach	stomach
13	chr19:38652200-38653800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:38652200-38653800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr19:38652200-38653800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
16	chr19:38652200-38653800	ZNF genes & repeats	Fetal Muscle Leg	muscle
17	chr19:38652200-38653800	ZNF genes & repeats	A549	lung
18	chr19:38652200-38653800	ZNF genes & repeats	Dnd41	blood
19	chr19:38652400-38653800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr19:38652400-38653800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
21	chr19:38652400-38653800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:38652400-38653800	ZNF genes & repeats	Adipose Nuclei	Adipose
23	chr19:38652400-38653800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
24	chr19:38652400-38653800	ZNF genes & repeats	Fetal Thymus	thymus
25	chr19:38652400-38653800	ZNF genes & repeats	Lung	lung
26	chr19:38652400-38653800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
27	chr19:38652400-38653800	ZNF genes & repeats	Thymus	Thymus
28	chr19:38652400-38653800	ZNF genes & repeats	Spleen	Spleen
29	chr19:38652400-38653800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
30	chr19:38652400-38654000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:38652400-38656400	Strong transcription	HepG2	liver
32	chr19:38652400-38657400	Strong transcription	Brain Angular Gyrus	brain
33	chr19:38652600-38653800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:38652600-38653800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:38652600-38653800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:38652600-38653800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr19:38652600-38653800	ZNF genes & repeats	Aorta	Aorta
38	chr19:38652600-38653800	ZNF genes & repeats	Brain Germinal Matrix	brain
39	chr19:38652600-38653800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
40	chr19:38652600-38653800	ZNF genes & repeats	Esophagus	oesophagus
41	chr19:38652600-38653800	ZNF genes & repeats	Fetal Brain Female	brain
42	chr19:38652600-38653800	ZNF genes & repeats	Fetal Lung	lung
43	chr19:38652600-38653800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
44	chr19:38652600-38654000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
45	chr19:38652600-38654000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:38652600-38654000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr19:38652600-38654000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:38652600-38654400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr19:38652600-38655800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr19:38652600-38656400	Strong transcription	iPS-15b Cell Line	embryonic stem cell

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