Variant report

Variant	rs4505809
Chromosome Location	chr4:26860413-26860414
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	IRF1	chr4:26858852-26860414	K562	blood:	n/a	chr4:26860092-26860105 chr4:26860064-26860084 chr4:26860091-26860105 chr4:26860207-26860223 chr4:26860060-26860074 chr4:26860068-26860082 chr4:26859190-26859204 chr4:26860066-26860080 chr4:26860058-26860078
2	POLR2A	chr4:26859063-26860891	K562	blood:	n/a	n/a
3	MAFF	chr4:26860171-26860875	K562	blood:	n/a	n/a
4	HCFC1	chr4:26858885-26860877	Hela-S3	cervix:	n/a	n/a
5	FOXA1	chr4:26860289-26860520	HepG2	liver:	n/a	n/a
6	ARID3A	chr4:26860284-26860859	K562	blood:	n/a	n/a
7	JUND	chr4:26858590-26860942	K562	blood:	n/a	n/a
8	POLR2A	chr4:26858643-26861233	PBDE	blood:	n/a	n/a
9	RCOR1	chr4:26860050-26861044	K562	blood:	n/a	n/a
10	KAP1	chr4:26860218-26861178	HEK293	kidney:	n/a	n/a
11	POLR2A	chr4:26858669-26861181	Raji	blood:	n/a	n/a
12	GATA1	chr4:26859064-26863326	PBDE	blood:	n/a	chr4:26859422-26859430 chr4:26861271-26861284 chr4:26859453-26859461 chr4:26861273-26861281
13	POLR2A	chr4:26858863-26860478	K562	blood:	n/a	n/a
14	POLR2A	chr4:26860292-26860420	K562	blood:	n/a	n/a
15	MXI1	chr4:26858240-26860638	SK-N-SH	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBC1D19-4	chr4:26859821-26860506	XLOC_003483
2	lnc-TBC1D19-4	chr4:26860235-26860539	XLOC_003483
3	lnc-TBC1D19-4	chr4:26860235-26860575	XLOC_003483

Variant related genes	Relation type
STIM2	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10029307	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11729927	0.90[ASN][1000 genomes]
rs11730235	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11734308	0.85[ASN][1000 genomes]
rs11737218	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11943948	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12641261	0.96[ASN][1000 genomes]
rs12644073	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12646473	0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12650172	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13116341	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13138942	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13139464	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28497454	0.89[ASN][1000 genomes]
rs28520489	0.87[ASN][1000 genomes]
rs34996346	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3792685	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs3924178	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4274829	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4407490	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.87[ASN][1000 genomes]
rs4519790	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4532223	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4557250	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4557251	0.94[ASN][1000 genomes]
rs57663175	0.88[ASN][1000 genomes]
rs57686546	0.89[ASN][1000 genomes]
rs58075729	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58968032	0.95[ASN][1000 genomes]
rs60890366	0.87[ASN][1000 genomes]
rs61047003	0.85[ASN][1000 genomes]
rs62302532	0.87[ASN][1000 genomes]
rs62302533	0.85[ASN][1000 genomes]
rs62302535	0.84[ASN][1000 genomes]
rs6448479	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6448484	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6448488	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6815719	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6833053	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6833895	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6835631	0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6844153	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6853032	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73116683	0.85[ASN][1000 genomes]
rs73811400	0.95[ASN][1000 genomes]
rs73813220	0.91[ASN][1000 genomes]
rs7655686	0.91[ASN][1000 genomes]
rs9790789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv470021	chr4:26721578-27067027	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1001306	chr4:26821511-26955344	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv461312	chr4:26844674-27078376	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv593872	chr4:26844674-27078376	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4505809	RP11-293A21.1	cis	Adipose Subcutaneous	GTEx
rs4505809	RP11-293A21.1	cis	Muscle Skeletal	GTEx
rs4505809	RP11-293A21.1	cis	Heart Left Ventricle	GTEx
rs4505809	RP11-293A21.1	cis	Skin Sun Exposed Lower leg	GTEx
rs4505809	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs4505809	STIM2	cis	multi-tissue	Pritchard
rs4505809	RP11-293A21.1	cis	Esophagus Muscularis	GTEx
rs4505809	STIM2	cis	lymphoblastoid	seeQTL
rs4505809	RP11-293A21.1	cis	lung	GTEx
rs4505809	RP11-293A21.1	cis	Thyroid	GTEx
rs4505809	RP11-293A21.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26858400-26860600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:26858600-26860600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:26858600-26860600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr4:26858600-26860600	Active TSS	K562	blood
5	chr4:26858600-26860800	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr4:26858600-26862800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:26858800-26861400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:26859400-26860600	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr4:26859400-26860600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:26859400-26860600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:26859400-26860600	Flanking Active TSS	HUVEC	blood vessel
12	chr4:26859400-26860600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr4:26859400-26860800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr4:26859400-26861000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr4:26859400-26862200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:26859600-26860600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:26859600-26860600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr4:26859600-26860600	Flanking Active TSS	Liver	Liver
19	chr4:26859600-26860600	Flanking Active TSS	Brain Angular Gyrus	brain
20	chr4:26859600-26860600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
21	chr4:26859600-26860600	Flanking Active TSS	Fetal Muscle Leg	muscle
22	chr4:26859600-26860600	Flanking Active TSS	Fetal Stomach	stomach
23	chr4:26859600-26860800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:26859600-26860800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:26859600-26860800	Flanking Active TSS	NH-A	brain
26	chr4:26859600-26861000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr4:26859600-26861000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr4:26859600-26861000	Flanking Active TSS	HSMM	muscle
29	chr4:26859600-26861400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:26859600-26861800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr4:26859600-26861800	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr4:26859600-26861800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr4:26859600-26862000	Flanking Active TSS	Fetal Thymus	thymus
34	chr4:26859800-26860600	Flanking Active TSS	Fetal Intestine Large	intestine
35	chr4:26859800-26860600	Flanking Active TSS	HSMMtube	muscle
36	chr4:26859800-26860800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr4:26859800-26860800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr4:26859800-26860800	Flanking Active TSS	Fetal Brain Female	brain
39	chr4:26859800-26860800	Flanking Active TSS	Fetal Lung	lung
40	chr4:26859800-26861000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr4:26859800-26861000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:26859800-26861000	Flanking Active TSS	NHLF	lung
43	chr4:26859800-26861800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:26859800-26861800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr4:26859800-26861800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr4:26859800-26861800	Enhancers	Spleen	Spleen
47	chr4:26859800-26862000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:26859800-26862000	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr4:26859800-26862000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr4:26859800-26862000	Flanking Active TSS	Dnd41	blood

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