Variant report

Variant	rs6853032
Chromosome Location	chr4:26858922-26858923
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	PML	chr4:26858724-26860055	GM12878	blood:	n/a	chr4:26860031-26860039
4	POLR2A	chr4:26858800-26859712	HL-60	blood:	n/a	n/a
5	ZNF143	chr4:26858901-26859548	GM12878	blood:	n/a	chr4:26859149-26859159
6	HCFC1	chr4:26858853-26859710	K562	blood:	n/a	n/a
7	POLR2A	chr4:26858902-26859572	K562	blood:	n/a	n/a
8	CREB1	chr4:26858838-26859736	HepG2	liver:	n/a	chr4:26859165-26859178
9	MTA3	chr4:26858576-26859224	GM12878	blood:	n/a	n/a
10	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
11	POLR2A	chr4:26858744-26859830	K562	blood:	n/a	n/a
12	HDAC2	chr4:26858863-26859453	H1-hESC	embryonic stem cell:	n/a	chr4:26859157-26859166
13	TEAD4	chr4:26858863-26859477	H1-hESC	embryonic stem cell:	n/a	n/a
14	GTF2F1	chr4:26858912-26859404	K562	blood:	n/a	n/a
15	POLR2A	chr4:26858845-26859691	HL-60	blood:	n/a	n/a
16	POLR2A	chr4:26858841-26859740	GM19193	blood:	n/a	n/a
17	TCF12	chr4:26858876-26859756	ECC-1	luminal epithelium:	n/a	chr4:26859015-26859023
18	YY1	chr4:26858920-26859540	SK-N-SH_RA	brain:	n/a	chr4:26859145-26859159 chr4:26859168-26859180 chr4:26859180-26859191 chr4:26859186-26859200
19	MAX	chr4:26858901-26859748	SK-N-SH	brain:	n/a	chr4:26859161-26859168 chr4:26859193-26859203 chr4:26859115-26859124 chr4:26859157-26859166
20	POLR2A	chr4:26858815-26859783	H1-neurons	neurons:	n/a	n/a
21	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
22	BHLHE40	chr4:26858606-26859615	K562	blood:	n/a	chr4:26859181-26859197 chr4:26859222-26859238 chr4:26859227-26859243
23	POLR2A	chr4:26858845-26859646	GM12878	blood:	n/a	n/a
24	POLR2A	chr4:26858844-26859755	U87	brain:	n/a	n/a
25	NFIC	chr4:26858842-26859721	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr4:26858834-26859488	GM12891	blood:	n/a	n/a
27	POLR2A	chr4:26858854-26860091	K562	blood:	n/a	n/a
28	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
29	POU2F2	chr4:26858841-26859475	GM12891	blood:	n/a	n/a
30	POLR2A	chr4:26858832-26859715	GM12892	blood:	n/a	n/a
31	POLR2A	chr4:26858850-26859681	Gliobla	brain:	n/a	n/a
32	RAD21	chr4:26858726-26859586	H1-hESC	embryonic stem cell:	n/a	chr4:26859166-26859185 chr4:26859276-26859285
33	HEY1	chr4:26858912-26859659	HepG2	liver:	n/a	chr4:26859177-26859192 chr4:26859223-26859238
34	POLR2A	chr4:26858895-26859635	GM12892	blood:	n/a	n/a
35	STAT5A	chr4:26858815-26859649	GM12878	blood:	n/a	chr4:26859443-26859455
36	MAZ	chr4:26858076-26859905	IMR90	lung:	n/a	chr4:26859161-26859168 chr4:26859193-26859203 chr4:26858393-26858406 chr4:26859115-26859124 chr4:26859157-26859166
37	RELA	chr4:26858775-26860121	GM10847	blood:	n/a	chr4:26859079-26859088 chr4:26859079-26859088
38	EGR1	chr4:26858806-26859619	HCT-116	colon:	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
39	BHLHE40	chr4:26858861-26859505	GM12878	blood:	n/a	chr4:26859181-26859197 chr4:26859222-26859238 chr4:26859227-26859243
40	POLR2A	chr4:26858917-26859178	GM12891	blood:	n/a	n/a
41	POLR2A	chr4:26858827-26859483	IMR90	lung:	n/a	n/a
42	SMC3	chr4:26858893-26859613	Hela-S3	cervix:	n/a	n/a
43	EP300	chr4:26858804-26859293	GM12878	blood:	n/a	chr4:26859150-26859159 chr4:26859180-26859196 chr4:26859143-26859159
44	POLR2A	chr4:26858818-26860369	GM12878	blood:	n/a	n/a
45	SIN3A	chr4:26858883-26860060	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr4:26858845-26859711	K562	blood:	n/a	n/a
47	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
48	GABPA	chr4:26858918-26859515	SK-N-SH	brain:	n/a	chr4:26859150-26859159 chr4:26859235-26859244 chr4:26859194-26859203
49	RELA	chr4:26858806-26859773	GM19193	blood:	n/a	chr4:26859079-26859088 chr4:26859079-26859088
50	MYC	chr4:26858897-26859866	K562	blood:	n/a	chr4:26859161-26859168 chr4:26859193-26859203 chr4:26859115-26859124 chr4:26859157-26859166

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:26858873-26858923	AG04449	skin:	fetal
2	chr4:26858873-26858923	GM12878	blood:	n/a
3	chr4:26858873-26858923	K562	blood:	n/a
4	chr4:26858873-26858923	GM12891	blood:	n/a
5	chr4:26858873-26858923	HAEpiC	amniotic membrane:	n/a
6	chr4:26858873-26858923	Caco-2	colon:	n/a
7	chr4:26858873-26858923	HPAEpiC	pulmonary alveolar:	n/a
8	chr4:26858873-26858923	IMR90	lung:	fetal
9	chr4:26858873-26858923	GM12892	blood:	n/a
10	chr4:26858873-26858923	AG04450	lung:	fetal
11	chr4:26858873-26858923	AG09319	gingival:	n/a
12	chr4:26858873-26858923	ECC-1	luminal epithelium:	n/a
13	chr4:26858873-26858923	HRPEpiC	eye:	n/a
14	chr4:26858873-26858923	HNPCEpiC	eye:	n/a
15	chr4:26858873-26858923	HCF	heart:	n/a
16	chr4:26858873-26858923	AoSMC	blood vessel:	n/a
17	chr4:26858873-26858923	HepG2	liver:	n/a
18	chr4:26858873-26858923	HEEpiC	esophagus:	n/a
19	chr4:26858873-26858923	SAEC	small airway:	n/a
20	chr4:26858873-26858923	HUVEC	blood vessel:	n/a
21	chr4:26858873-26858923	BJ	skin:	n/a
22	chr4:26858873-26858923	PANC-1	pancreas:	n/a
23	chr4:26858873-26858923	MCF10A-Er-Src	breast:	n/a
24	chr4:26858873-26858923	BE2_C	brain:	n/a
25	chr4:26858873-26858923	SKMC	muscle:	n/a
26	chr4:26858873-26858923	GM19239	blood:	n/a
27	chr4:26858873-26858923	HIPEpiC	eye:	n/a
28	chr4:26858873-26858923	NB4	blood:	n/a
29	chr4:26858873-26858923	Hepatocyte	liver:	n/a
30	chr4:26858873-26858923	HCT-116	colon:	n/a
31	chr4:26858873-26858923	PrEC	prostate:	n/a
32	chr4:26858873-26858923	HRCEpiC	kidney:	n/a
33	chr4:26858873-26858923	HCM	heart:	n/a
34	chr4:26858873-26858923	LNCaP	prostate:	n/a
35	chr4:26858873-26858923	NHDF-neo	bronchial:	n/a
36	chr4:26858873-26858923	NH-A	brain:	n/a
37	chr4:26858873-26858923	ProgFib	skin:	n/a
38	chr4:26858873-26858923	CMK	blood:	n/a
39	chr4:26858873-26858923	HRE	kidney:	n/a
40	chr4:26858873-26858923	T-47D	breast:	n/a
41	chr4:26858873-26858923	NT2-D1	testis:	n/a
42	chr4:26858873-26858923	PFSK-1	brain:	n/a
43	chr4:26858873-26858923	HEK293	kidney:	embryo
44	chr4:26858873-26858923	Hela-S3	cervix:	n/a
45	chr4:26858873-26858923	HCPEpiC	choroid plexus:	n/a
46	chr4:26858873-26858923	MCF-7	breast:	n/a
47	chr4:26858873-26858923	U87	brain:	n/a
48	chr4:26858873-26858923	AG10803	skin:	n/a
49	chr4:26858873-26858923	A549	lung:	n/a
50	chr4:26858873-26858923	Jurkat	blood:	n/a

Variant related genes	Relation type
STIM2	TF binding region
STIM2	CpG island

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	0.89[ASN][1000 genomes]
rs11730235	0.89[ASN][1000 genomes]
rs11734308	0.85[ASN][1000 genomes]
rs11737218	0.94[ASN][1000 genomes]
rs11943948	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12641261	0.94[ASN][1000 genomes]
rs12644073	0.90[ASN][1000 genomes]
rs12646473	0.94[ASN][1000 genomes]
rs12650172	0.94[ASN][1000 genomes]
rs13116341	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13138942	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13139464	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28497454	0.88[ASN][1000 genomes]
rs28520489	0.87[ASN][1000 genomes]
rs34996346	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3792685	0.82[ASN][1000 genomes]
rs3924178	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4274829	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4407490	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4505809	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4519790	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4532223	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4557250	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4557251	0.91[ASN][1000 genomes]
rs57663175	0.87[ASN][1000 genomes]
rs57686546	0.89[ASN][1000 genomes]
rs58075729	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58968032	0.94[ASN][1000 genomes]
rs60890366	0.86[ASN][1000 genomes]
rs61047003	0.85[ASN][1000 genomes]
rs62302532	0.86[ASN][1000 genomes]
rs62302533	0.85[ASN][1000 genomes]
rs62302535	0.83[ASN][1000 genomes]
rs6448479	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6448484	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6448488	0.85[ASN][1000 genomes]
rs6815719	0.94[ASN][1000 genomes]
rs6833053	0.94[ASN][1000 genomes]
rs6833895	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6835631	0.86[ASN][1000 genomes]
rs6844153	0.86[ASN][1000 genomes]
rs73116683	0.84[ASN][1000 genomes]
rs73811400	0.94[ASN][1000 genomes]
rs73813220	0.90[ASN][1000 genomes]
rs7655686	0.91[ASN][1000 genomes]
rs9790789	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[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
rs6853032	RP11-293A21.1	cis	lung	GTEx
rs6853032	RP11-293A21.1	cis	Adipose Subcutaneous	GTEx
rs6853032	RP11-293A21.1	cis	Esophagus Mucosa	GTEx
rs6853032	RP11-293A21.1	cis	Muscle Skeletal	GTEx
rs6853032	RP11-293A21.1	cis	Thyroid	GTEx
rs6853032	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs6853032	RP11-293A21.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26858400-26859000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
2	chr4:26858400-26859000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr4:26858400-26859000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:26858400-26859000	Flanking Active TSS	Dnd41	blood
5	chr4:26858400-26859600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr4:26858400-26859800	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr4:26858400-26859800	Active TSS	Thymus	Thymus
8	chr4:26858400-26860000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:26858400-26860200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr4:26858400-26860600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr4:26858600-26859000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr4:26858600-26859000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr4:26858600-26859000	Flanking Active TSS	Primary B cells from peripheral blood	blood
14	chr4:26858600-26859000	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr4:26858600-26859000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr4:26858600-26859000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr4:26858600-26859000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr4:26858600-26859000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr4:26858600-26859000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr4:26858600-26859000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr4:26858600-26859000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:26858600-26859000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:26858600-26859000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr4:26858600-26859000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr4:26858600-26859000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:26858600-26859000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:26858600-26859000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr4:26858600-26859000	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr4:26858600-26859000	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr4:26858600-26859000	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr4:26858600-26859000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr4:26858600-26859000	Flanking Active TSS	Fetal Thymus	thymus
33	chr4:26858600-26859000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr4:26858600-26859000	Flanking Active TSS	Stomach Mucosa	stomach
35	chr4:26858600-26859000	Flanking Active TSS	Hela-S3	cervix
36	chr4:26858600-26859000	Flanking Bivalent TSS/Enh	HepG2	liver
37	chr4:26858600-26859000	Flanking Active TSS	HMEC	breast
38	chr4:26858600-26859000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr4:26858600-26859000	Flanking Active TSS	NH-A	brain
40	chr4:26858600-26859000	Flanking Active TSS	NHEK	skin
41	chr4:26858600-26859400	Active TSS	H1 Cell Line	embryonic stem cell
42	chr4:26858600-26859400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:26858600-26859400	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr4:26858600-26859400	Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr4:26858600-26859600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:26858600-26859600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:26858600-26859600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:26858600-26859600	Active TSS	Liver	Liver
49	chr4:26858600-26859600	Active TSS	Brain Hippocampus Middle	brain
50	chr4:26858600-26859600	Active TSS	Brain Inferior Temporal Lobe	brain

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