Variant report

Variant	rs6448484
Chromosome Location	chr4:26859258-26859259
allele	C/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	FOXM1	chr4:26858761-26859373	GM12878	blood:	n/a	n/a
2	GABPA	chr4:26858908-26859670	K562	blood:	n/a	chr4:26859150-26859159 chr4:26859235-26859244 chr4:26859194-26859203
3	POLR2A	chr4:26858941-26859955	HCT-116	colon:	n/a	n/a
4	PML	chr4:26858724-26860055	GM12878	blood:	n/a	chr4:26860031-26860039
5	PAX5	chr4:26859006-26859502	GM12878	blood:	n/a	n/a
6	POLR2A	chr4:26858800-26859712	HL-60	blood:	n/a	n/a
7	ZNF143	chr4:26858901-26859548	GM12878	blood:	n/a	chr4:26859149-26859159
8	POLR2A	chr4:26859133-26859528	H1-hESC	embryonic stem cell:	n/a	n/a
9	HCFC1	chr4:26858853-26859710	K562	blood:	n/a	n/a
10	RCOR1	chr4:26858965-26859751	K562	blood:	n/a	n/a
11	POLR2A	chr4:26858902-26859572	K562	blood:	n/a	n/a
12	CTCF	chr4:26859076-26859263	GM12892	blood:	n/a	chr4:26859169-26859185
13	CREB1	chr4:26858838-26859736	HepG2	liver:	n/a	chr4:26859165-26859178
14	EGR1	chr4:26858907-26859500	H1-hESC	embryonic stem cell:	n/a	chr4:26859154-26859168 chr4:26859192-26859206 chr4:26859152-26859166 chr4:26859150-26859172 chr4:26859156-26859165 chr4:26859155-26859168 chr4:26859156-26859167 chr4:26859156-26859166 chr4:26859193-26859203 chr4:26859149-26859159 chr4:26859155-26859168 chr4:26859156-26859166 chr4:26859155-26859168
15	POLR2A	chr4:26858744-26859830	K562	blood:	n/a	n/a
16	TAF1	chr4:26859140-26859566	H1-hESC	embryonic stem cell:	n/a	n/a
17	PAX5	chr4:26859112-26859357	GM12891	blood:	n/a	n/a
18	TAF1	chr4:26859102-26859533	SK-N-SH	brain:	n/a	n/a
19	HDAC2	chr4:26858863-26859453	H1-hESC	embryonic stem cell:	n/a	chr4:26859157-26859166
20	TEAD4	chr4:26858863-26859477	H1-hESC	embryonic stem cell:	n/a	n/a
21	GTF2F1	chr4:26858912-26859404	K562	blood:	n/a	n/a
22	YY1	chr4:26858933-26859641	ECC-1	luminal epithelium:	n/a	chr4:26859145-26859159 chr4:26859168-26859180 chr4:26859180-26859191 chr4:26859186-26859200
23	POLR2A	chr4:26858845-26859691	HL-60	blood:	n/a	n/a
24	POLR2A	chr4:26858841-26859740	GM19193	blood:	n/a	n/a
25	TCF12	chr4:26858876-26859756	ECC-1	luminal epithelium:	n/a	chr4:26859015-26859023
26	EBF1	chr4:26858981-26859343	GM12878	blood:	n/a	n/a
27	BRCA1	chr4:26859135-26859403	HepG2	liver:	n/a	n/a
28	YY1	chr4:26858920-26859540	SK-N-SH_RA	brain:	n/a	chr4:26859145-26859159 chr4:26859168-26859180 chr4:26859180-26859191 chr4:26859186-26859200
29	MYC	chr4:26859040-26859671	MCF-7	breast:	n/a	chr4:26859161-26859168 chr4:26859193-26859203 chr4:26859115-26859124 chr4:26859157-26859166
30	MAX	chr4:26858901-26859748	SK-N-SH	brain:	n/a	chr4:26859161-26859168 chr4:26859193-26859203 chr4:26859115-26859124 chr4:26859157-26859166
31	RFX5	chr4:26858992-26859524	GM12878	blood:	n/a	n/a
32	CTCF	chr4:26859100-26859413	Spleen_OC	spleen:	n/a	chr4:26859169-26859185
33	E2F4	chr4:26858974-26859562	K562	blood:	n/a	chr4:26859150-26859159 chr4:26859506-26859520
34	POLR2A	chr4:26858815-26859783	H1-neurons	neurons:	n/a	n/a
35	EGR1	chr4:26858807-26859498	ECC-1	luminal epithelium:	n/a	chr4:26859154-26859168 chr4:26859192-26859206 chr4:26859152-26859166 chr4:26859150-26859172 chr4:26859156-26859165 chr4:26859155-26859168 chr4:26859156-26859167 chr4:26859156-26859166 chr4:26859193-26859203 chr4:26859149-26859159 chr4:26859155-26859168 chr4:26859156-26859166 chr4:26859155-26859168
36	BHLHE40	chr4:26858606-26859615	K562	blood:	n/a	chr4:26859181-26859197 chr4:26859222-26859238 chr4:26859227-26859243
37	POLR2A	chr4:26858845-26859646	GM12878	blood:	n/a	n/a
38	NRF1	chr4:26859202-26859464	HepG2	liver:	n/a	chr4:26859301-26859312 chr4:26859323-26859334 chr4:26859235-26859244
39	POLR2A	chr4:26858844-26859755	U87	brain:	n/a	n/a
40	NFIC	chr4:26858842-26859721	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr4:26858834-26859488	GM12891	blood:	n/a	n/a
42	GABPA	chr4:26859049-26859405	HepG2	liver:	n/a	chr4:26859150-26859159 chr4:26859235-26859244 chr4:26859194-26859203
43	GABPA	chr4:26859020-26859476	H1-hESC	embryonic stem cell:	n/a	chr4:26859150-26859159 chr4:26859235-26859244 chr4:26859194-26859203
44	POLR2A	chr4:26858854-26860091	K562	blood:	n/a	n/a
45	NRF1	chr4:26858629-26859678	SK-N-SH	brain:	n/a	chr4:26859150-26859159 chr4:26859301-26859312 chr4:26859323-26859334 chr4:26859235-26859244 chr4:26859194-26859203
46	POU2F2	chr4:26858841-26859475	GM12891	blood:	n/a	n/a
47	POLR2A	chr4:26858832-26859715	GM12892	blood:	n/a	n/a
48	REST	chr4:26859122-26859598	HL-60	blood:	n/a	chr4:26859124-26859137
49	PAX5	chr4:26859059-26859300	GM12878	blood:	n/a	n/a
50	POLR2A	chr4:26858850-26859681	Gliobla	brain:	n/a	n/a

Variant related genes	Relation type
STIM2	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10029307	0.89[ASN][1000 genomes]
rs11729927	0.90[ASN][1000 genomes]
rs11730235	0.90[ASN][1000 genomes]
rs11734308	0.85[ASN][1000 genomes]
rs11737218	0.95[ASN][1000 genomes]
rs11943948	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12641261	0.96[ASN][1000 genomes]
rs12644073	0.91[ASN][1000 genomes]
rs12646473	0.96[ASN][1000 genomes]
rs12650172	0.96[ASN][1000 genomes]
rs13116341	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13138942	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13139464	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28497454	0.89[ASN][1000 genomes]
rs28520489	0.87[ASN][1000 genomes]
rs34996346	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3792685	0.82[ASN][1000 genomes]
rs3924178	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4274829	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4407490	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4505809	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519790	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4532223	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4557250	0.81[AMR][1000 genomes];0.91[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	0.87[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	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6448488	0.85[ASN][1000 genomes]
rs6815719	0.96[ASN][1000 genomes]
rs6833053	0.96[ASN][1000 genomes]
rs6833895	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6835631	0.87[ASN][1000 genomes]
rs6844153	0.87[ASN][1000 genomes]
rs6853032	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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	0.89[AMR][1000 genomes];0.94[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6448484	RP11-293A21.1	cis	lung	GTEx
rs6448484	RP11-293A21.1	cis	Skin Sun Exposed Lower leg	GTEx
rs6448484	RP11-293A21.1	cis	Esophagus Mucosa	GTEx
rs6448484	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs6448484	RP11-293A21.1	cis	Adipose Subcutaneous	GTEx
rs6448484	RP11-293A21.1	cis	Muscle Skeletal	GTEx
rs6448484	RP11-293A21.1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26858400-26859600	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr4:26858400-26859800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr4:26858400-26859800	Active TSS	Thymus	Thymus
4	chr4:26858400-26860000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:26858400-26860200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr4:26858400-26860600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr4:26858600-26859400	Active TSS	H1 Cell Line	embryonic stem cell
8	chr4:26858600-26859400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:26858600-26859400	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr4:26858600-26859400	Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr4:26858600-26859600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:26858600-26859600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:26858600-26859600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:26858600-26859600	Active TSS	Liver	Liver
15	chr4:26858600-26859600	Active TSS	Brain Hippocampus Middle	brain
16	chr4:26858600-26859600	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr4:26858600-26859600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:26858600-26859600	Active TSS	Brain Substantia Nigra	brain
19	chr4:26858600-26859600	Active TSS	Colon Smooth Muscle	Colon
20	chr4:26858600-26859600	Active TSS	Fetal Brain Male	brain
21	chr4:26858600-26859600	Active TSS	Fetal Intestine Small	intestine
22	chr4:26858600-26859600	Active TSS	Fetal Muscle Trunk	muscle
23	chr4:26858600-26859600	Active TSS	Fetal Muscle Leg	muscle
24	chr4:26858600-26859600	Active TSS	Placenta	Placenta
25	chr4:26858600-26859600	Active TSS	Fetal Stomach	stomach
26	chr4:26858600-26859600	Active TSS	Stomach Smooth Muscle	stomach
27	chr4:26858600-26859600	Active TSS	Osteobl	bone
28	chr4:26858600-26859800	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr4:26858600-26859800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:26858600-26859800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:26858600-26859800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:26858600-26859800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr4:26858600-26859800	Active TSS	Brain Germinal Matrix	brain
34	chr4:26858600-26859800	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr4:26858600-26859800	Active TSS	Fetal Intestine Large	intestine
36	chr4:26858600-26859800	Active TSS	Fetal Kidney	kidney
37	chr4:26858600-26859800	Active TSS	Fetal Lung	lung
38	chr4:26858600-26859800	Active TSS	Rectal Smooth Muscle	rectum
39	chr4:26858600-26859800	Active TSS	Right Atrium	heart
40	chr4:26858600-26859800	Active TSS	NHDF-Ad	bronchial
41	chr4:26858600-26859800	Active TSS	NHLF	lung
42	chr4:26858600-26860000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr4:26858600-26860000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:26858600-26860000	Active TSS	Colonic Mucosa	Colon
45	chr4:26858600-26860200	Active TSS	GM12878-XiMat	blood
46	chr4:26858600-26860400	Active TSS	A549	lung
47	chr4:26858600-26860600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:26858600-26860600	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr4:26858600-26860600	Active TSS	K562	blood
50	chr4:26858600-26860800	Flanking Active TSS	Primary hematopoietic stem cells	blood

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