Variant report

Variant	rs223391
Chromosome Location	chr4:103748224-103748225
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	POLR2A	chr4:103747681-103749825	HUVEC	blood vessel:	n/a	n/a
2	HEY1	chr4:103747721-103749756	HepG2	liver:	n/a	chr4:103748332-103748347
3	POLR2A	chr4:103747377-103749984	HL-60	blood:	n/a	n/a
4	BCLAF1	chr4:103747444-103750011	GM12878	blood:	n/a	chr4:103748724-103748733 chr4:103749806-103749815
5	POLR2A	chr4:103747602-103749671	GM10847	blood:	n/a	n/a
6	SIN3AK20	chr4:103747794-103749706	MCF-7	breast:	n/a	n/a
7	TAF1	chr4:103747860-103748401	GM12892	blood:	n/a	n/a
8	E2F4	chr4:103748017-103749685	MCF10A-Er-Src	breast:	n/a	chr4:103749343-103749357
9	POLR2A	chr4:103747795-103749750	A549	lung:	n/a	n/a
10	SIN3AK20	chr4:103747756-103749962	HCT-116	colon:	n/a	n/a
11	TCF12	chr4:103747781-103749846	ECC-1	luminal epithelium:	n/a	chr4:103748203-103748210 chr4:103748186-103748193
12	NFIC	chr4:103747608-103748327	GM12878	blood:	n/a	n/a
13	CHD2	chr4:103747865-103749755	K562	blood:	n/a	chr4:103748391-103748401 chr4:103748142-103748152
14	POLR2A	chr4:103747794-103749794	MCF-7	breast:	n/a	n/a
15	POLR2A	chr4:103747555-103749909	K562	blood:	n/a	n/a
16	SIN3A	chr4:103747781-103749757	GM12878	blood:	n/a	chr4:103748885-103748893 chr4:103748507-103748518
17	BHLHE40	chr4:103747970-103749844	HepG2	liver:	n/a	n/a
18	BCL3	chr4:103748093-103748919	K562	blood:	n/a	chr4:103748724-103748733
19	STAT3	chr4:103747913-103748324	MCF10A-Er-Src	breast:	n/a	chr4:103748184-103748195 chr4:103748024-103748036
20	ZBTB33	chr4:103747805-103749729	SK-N-SH	brain:	n/a	chr4:103749692-103749701 chr4:103748325-103748335
21	CHD2	chr4:103747731-103749947	GM12878	blood:	n/a	chr4:103748391-103748401 chr4:103748142-103748152
22	FOXM1	chr4:103747599-103749846	GM12878	blood:	n/a	n/a
23	GABPA	chr4:103747792-103748308	MCF-7	breast:	n/a	n/a
24	CEBPB	chr4:103748170-103749687	HepG2	liver:	n/a	n/a
25	POLR2A	chr4:103746212-103750739	MCF10A-Er-Src	breast:	n/a	n/a
26	TAF1	chr4:103748208-103749728	HepG2	liver:	n/a	n/a
27	NFATC1	chr4:103747587-103749951	GM12878	blood:	n/a	n/a
28	MYBL2	chr4:103747828-103750090	HepG2	liver:	n/a	n/a
29	STAT1	chr4:103747901-103749750	GM12878	blood:	n/a	chr4:103748184-103748195 chr4:103748548-103748560 chr4:103748931-103748943 chr4:103748725-103748737 chr4:103748024-103748036 chr4:103748926-103748938
30	TBP	chr4:103747894-103749898	GM12878	blood:	n/a	n/a
31	ETS1	chr4:103747889-103749026	K562	blood:	n/a	chr4:103749006-103749015 chr4:103747957-103747968 chr4:103749007-103749016 chr4:103748730-103748741
32	ARID3A	chr4:103748083-103749793	HepG2	liver:	n/a	n/a
33	POLR2A	chr4:103747624-103749965	HUVEC	blood vessel:	n/a	n/a
34	GATA1	chr4:103748123-103749886	PBDE	blood:	n/a	chr4:103748221-103748231
35	CTCF	chr4:103747922-103748289	K562	blood:	n/a	n/a
36	IRF1	chr4:103747922-103749664	K562	blood:	n/a	chr4:103748183-103748203 chr4:103748184-103748197 chr4:103748185-103748199 chr4:103748184-103748195 chr4:103748184-103748198 chr4:103748184-103748197 chr4:103748184-103748197 chr4:103748184-103748197
37	BRCA1	chr4:103747957-103749545	GM12878	blood:	n/a	n/a
38	CBX3	chr4:103747671-103749880	HCT-116	colon:	n/a	n/a
39	RELA	chr4:103747844-103749812	GM19193	blood:	n/a	n/a
40	CTCF	chr4:103748100-103748250	HRE	kidney:	n/a	n/a
41	TCF12	chr4:103747795-103749838	ECC-1	luminal epithelium:	n/a	chr4:103748203-103748210 chr4:103748186-103748193
42	POLR2A	chr4:103747864-103749717	HepG2	liver:	n/a	n/a
43	SMC3	chr4:103747934-103749895	Hela-S3	cervix:	n/a	chr4:103748919-103748927
44	MAX	chr4:103748007-103749808	A549	lung:	n/a	chr4:103748924-103748934 chr4:103749588-103749599 chr4:103749588-103749599 chr4:103749061-103749070 chr4:103749590-103749597 chr4:103749589-103749598
45	JUND	chr4:103747987-103749810	H1-hESC	embryonic stem cell:	n/a	chr4:103748277-103748287 chr4:103748222-103748231 chr4:103749654-103749666
46	RUNX3	chr4:103747601-103749960	GM12878	blood:	n/a	n/a
47	POLR2A	chr4:103746375-103750078	SK-N-MC	brain:	n/a	n/a
48	POLR2A	chr4:103746789-103749912	GM12891	blood:	n/a	n/a
49	TEAD4	chr4:103748139-103749802	K562	blood:	n/a	n/a
50	NFATC1	chr4:103747332-103749923	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:103419348..103423957-chr4:103746554..103750456,7	MCF-7	breast:
2	chr4:103730843..103736706-chr4:103746374..103749972,8	MCF-7	breast:
3	chr4:103421566..103424767-chr4:103746039..103749014,5	K562	blood:
4	chr4:103747245..103749359-chr4:103986696..103989097,2	K562	blood:
5	chr4:103264289..103266526-chr4:103747342..103750313,2	K562	blood:
6	chr4:103747527..103750862-chr4:103937830..103941231,4	MCF-7	breast:
7	chr4:103747144..103749225-chr4:103996606..103998315,2	K562	blood:
8	chr4:103650888..103653325-chr4:103747345..103748932,2	MCF-7	breast:
9	chr4:103746553..103755574-chr4:103787108..103794302,29	MCF-7	breast:
10	chr4:103670492..103673168-chr4:103747982..103750362,2	K562	blood:
11	chr12:125399204..125400059-chr4:103747951..103748729,2	Hela-S3	cervix:
12	chr4:103680041..103683633-chr4:103747125..103750295,6	MCF-7	breast:
13	chr4:103723421..103727498-chr4:103747024..103749804,3	MCF-7	breast:
14	chr4:103721670..103724216-chr4:103745688..103748268,3	MCF-7	breast:
15	chr4:103747413..103749606-chr4:103996961..103999341,3	MCF-7	breast:
16	chr4:103745482..103752084-chr4:103788371..103792114,20	MCF-7	breast:
17	chr4:103649437..103652154-chr4:103748194..103749901,2	K562	blood:
18	chr4:103736995..103756245-chr4:103778393..103800311,117	K562	blood:
19	chr4:100871315..100874297-chr4:103746830..103749271,3	K562	blood:
20	chr4:103422194..103424603-chr4:103745115..103749014,4	K562	blood:
21	chr4:100870517..100873586-chr4:103747603..103750269,4	K562	blood:
22	chr2:70316209..70318717-chr4:103747882..103750776,2	MCF-7	breast:
23	chr4:103422470..103425654-chr4:103747796..103750322,3	MCF-7	breast:
24	chr4:103741330..103752134-chr4:103778393..103796398,92	K562	blood:

Variant related genes	Relation type
UBE2D3	TF binding region
ENSG00000246560	TF binding region
ENSG00000230069	Chromatin interaction
ENSG00000145354	Chromatin interaction
ENSG00000238948	Chromatin interaction
ENSG00000164032	Chromatin interaction
ENSG00000164038	Chromatin interaction
ENSG00000248971	Chromatin interaction
ENSG00000164037	Chromatin interaction
ENSG00000233060	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000150991	Chromatin interaction
ENSG00000260651	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000109320	Chromatin interaction
ENSG00000251288	Chromatin interaction
ENSG00000109323	Chromatin interaction
ENSG00000138821	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10516497	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs13112128	0.80[JPT][hapmap]
rs223408	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs223495	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap]
rs223496	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs223499	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs223500	0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap]
rs223501	0.80[JPT][hapmap]
rs223504	0.80[JPT][hapmap]
rs223508	0.80[JPT][hapmap]
rs223510	0.80[JPT][hapmap]
rs227285	0.80[JPT][hapmap]
rs227369	0.80[JPT][hapmap]
rs227372	0.80[JPT][hapmap]
rs9994654	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594957	chr4:103728010-103870091	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs223391	KRT8P46	cis	lung	GTEx
rs223391	KRT8P46	cis	Esophagus Mucosa	GTEx
rs223391	CENPE	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103742000-103750200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr4:103742600-103748400	Active TSS	Right Atrium	heart
3	chr4:103742800-103748800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:103743200-103750000	Active TSS	Aorta	Aorta
5	chr4:103743600-103750200	Active TSS	NHLF	lung
6	chr4:103744000-103750400	Active TSS	Right Ventricle	heart
7	chr4:103744200-103748800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:103744200-103749600	Active TSS	Primary T cells fromperipheralblood	blood
9	chr4:103744400-103748600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
10	chr4:103744400-103750000	Active TSS	Ovary	ovary
11	chr4:103744400-103750200	Active TSS	Left Ventricle	heart
12	chr4:103744400-103750200	Active TSS	HSMMtube	muscle
13	chr4:103744400-103750400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:103744600-103749600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:103744600-103749600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:103744800-103750400	Active TSS	Colonic Mucosa	Colon
17	chr4:103744800-103750600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:103745000-103749800	Active TSS	Lung	lung
19	chr4:103745000-103750000	Active TSS	Sigmoid Colon	Sigmoid Colon
20	chr4:103745000-103750200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:103745200-103750200	Active TSS	HMEC	breast
22	chr4:103745200-103750200	Active TSS	NHDF-Ad	bronchial
23	chr4:103745200-103750400	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr4:103745400-103749800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:103745400-103749800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:103745400-103749800	Active TSS	Stomach Smooth Muscle	stomach
27	chr4:103745400-103750200	Active TSS	A549	lung
28	chr4:103745400-103750200	Active TSS	Hela-S3	cervix
29	chr4:103745400-103750400	Active TSS	GM12878-XiMat	blood
30	chr4:103745400-103750800	Active TSS	H9 Cell Line	embryonic stem cell
31	chr4:103745600-103749800	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr4:103745600-103750000	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr4:103745800-103748600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr4:103745800-103749600	Active TSS	Adipose Nuclei	Adipose
35	chr4:103745800-103749600	Active TSS	Placenta	Placenta
36	chr4:103745800-103749600	Active TSS	NH-A	brain
37	chr4:103745800-103749800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:103745800-103750000	Active TSS	Fetal Muscle Trunk	muscle
39	chr4:103745800-103750200	Active TSS	Fetal Intestine Large	intestine
40	chr4:103745800-103750200	Active TSS	Psoas Muscle	Psoas
41	chr4:103745800-103750400	Active TSS	H1 Cell Line	embryonic stem cell
42	chr4:103745800-103750400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:103746000-103749400	Active TSS	Fetal Thymus	thymus
44	chr4:103746000-103749600	Active TSS	Primary monocytes fromperipheralblood	blood
45	chr4:103746000-103749600	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr4:103746000-103749600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr4:103746000-103749600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:103746000-103749600	Active TSS	Liver	Liver
49	chr4:103746000-103749600	Active TSS	Brain Angular Gyrus	brain
50	chr4:103746000-103749600	Active TSS	Brain Anterior Caudate	brain

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