Variant report

Variant	rs28458175
Chromosome Location	chr14:55369421-55369422
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	ZEB1	chr14:55369337-55369578	GM12878	blood:	n/a	n/a
2	HCFC1	chr14:55368972-55370036	K562	blood:	n/a	n/a
3	TAF1	chr14:55369409-55369608	GM12891	blood:	n/a	n/a
4	MAX	chr14:55369377-55369952	A549	lung:	n/a	n/a
5	YY1	chr14:55368649-55370176	HepG2	liver:	n/a	chr14:55368997-55369006 chr14:55368995-55369009 chr14:55368994-55369003 chr14:55368994-55369005
6	MAX	chr14:55368718-55370023	GM12878	blood:	n/a	n/a
7	TAF1	chr14:55369400-55369841	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr14:55369297-55369632	U87	brain:	n/a	n/a
9	POLR2A	chr14:55369169-55369653	HUVEC	blood vessel:	n/a	n/a
10	BHLHE40	chr14:55368855-55369669	GM12878	blood:	n/a	chr14:55368993-55369009
11	POLR2A	chr14:55368696-55369898	GM10847	blood:	n/a	n/a
12	CREB1	chr14:55368629-55370149	HepG2	liver:	n/a	n/a
13	TAF1	chr14:55369308-55369675	K562	blood:	n/a	n/a
14	POLR2A	chr14:55368542-55369931	GM12892	blood:	n/a	n/a
15	NFYB	chr14:55369402-55369833	Hela-S3	cervix:	n/a	chr14:55369603-55369618 chr14:55369604-55369618 chr14:55369603-55369618
16	POLR2A	chr14:55369297-55369657	U87	brain:	n/a	n/a
17	POLR2A	chr14:55369330-55369612	A549	lung:	n/a	n/a
18	POLR2A	chr14:55369343-55369658	A549	lung:	n/a	n/a
19	MAX	chr14:55368526-55370167	Hela-S3	cervix:	n/a	n/a
20	GATA3	chr14:55368282-55370167	MCF-7	breast:	n/a	n/a
21	CTCF	chr14:55369340-55369490	Hela-S3	cervix:	n/a	n/a
22	EP300	chr14:55369360-55369713	T-47D	breast:	n/a	n/a
23	ELF1	chr14:55368402-55370087	GM12878	blood:	n/a	chr14:55369656-55369668
24	POU2F2	chr14:55369352-55369609	GM12878	blood:	n/a	n/a
25	GATA1	chr14:55369240-55369818	PBDE	blood:	n/a	n/a
26	CREB1	chr14:55369324-55370147	GM12878	blood:	n/a	n/a
27	ZKSCAN1	chr14:55368614-55370022	Hela-S3	cervix:	n/a	n/a
28	PML	chr14:55368587-55369873	MCF-7	breast:	n/a	n/a
29	JUND	chr14:55369352-55369650	HepG2	liver:	n/a	chr14:55369605-55369614
30	CREB1	chr14:55369284-55370176	HepG2	liver:	n/a	n/a
31	POLR2A	chr14:55369293-55369620	PFSK-1	brain:	n/a	n/a
32	RCOR1	chr14:55368602-55370024	Hela-S3	cervix:	n/a	n/a
33	NFIC	chr14:55368656-55369741	ECC-1	luminal epithelium:	n/a	n/a
34	CTCF	chr14:55369349-55370298	K562	blood:	n/a	chr14:55370049-55370067 chr14:55369674-55369683 chr14:55369671-55369689
35	TBP	chr14:55368639-55370148	K562	blood:	n/a	n/a
36	POLR2A	chr14:55368645-55369828	GM12878	blood:	n/a	n/a
37	E2F1	chr14:55368551-55369983	Hela-S3	cervix:	n/a	chr14:55368932-55368940 chr14:55369556-55369565 chr14:55368997-55369006 chr14:55369654-55369666 chr14:55368783-55368795 chr14:55368933-55368940 chr14:55368884-55368895 chr14:55369613-55369623
38	POLR2A	chr14:55369295-55369723	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr14:55368707-55370002	HepG2	liver:	n/a	n/a
40	CREB1	chr14:55369317-55370131	H1-hESC	embryonic stem cell:	n/a	n/a
41	MYC	chr14:55368716-55370077	K562	blood:	n/a	n/a
42	POLR2A	chr14:55368697-55369893	SK-N-MC	brain:	n/a	n/a
43	YY1	chr14:55369373-55369680	HCT-116	colon:	n/a	n/a
44	BRCA1	chr14:55369321-55369517	Hela-S3	cervix:	n/a	n/a
45	MAX	chr14:55368459-55370154	ECC-1	luminal epithelium:	n/a	n/a
46	MAFK	chr14:55368931-55370066	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr14:55369154-55369770	HUVEC	blood vessel:	n/a	n/a
48	TCF7L2	chr14:55368818-55370215	HCT-116	colon:	n/a	chr14:55370156-55370166
49	HDAC2	chr14:55368733-55370089	HepG2	liver:	n/a	n/a
50	POLR2A	chr14:55368734-55370227	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:55368060..55369582-chr14:55493883..55496744,2	MCF-7	breast:
2	chr14:55368751..55370631-chr14:55518308..55520538,2	K562	blood:
3	chr14:55368974..55369574-chr6:27100348..27100871,2	Hela-S3	cervix:
4	chr14:55368311..55371330-chr14:55594542..55598408,4	MCF-7	breast:
5	chr14:55030801..55036234-chr14:55366700..55372024,9	MCF-7	breast:
6	chr14:55343213..55346860-chr14:55368496..55370471,3	MCF-7	breast:
7	chr14:55247890..55252413-chr14:55368163..55370491,5	MCF-7	breast:
8	chr14:55351951..55354870-chr14:55368126..55370512,5	MCF-7	breast:
9	chr14:55367425..55371142-chr14:55516489..55521777,7	MCF-7	breast:
10	chr14:55369172..55369944-chr19:35264069..35264965,2	HCT-116	colon:
11	chr14:55032369..55034172-chr14:55367637..55369968,2	K562	blood:
12	chr14:55368105..55371463-chr14:55516987..55520396,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SAMD4A-3	chr14:55369024-55370518	NONHSAT036977

Variant related genes	Relation type
GCH1	TF binding region
ENSG00000180008	Chromatin interaction
ENSG00000153896	Chromatin interaction
ENSG00000265432	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000020577	Chromatin interaction
ENSG00000131981	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000168175	Chromatin interaction
ENSG00000258872	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10143699	0.82[AFR][1000 genomes]
rs10148995	0.82[AFR][1000 genomes]
rs11847085	0.87[AFR][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	nsv530042	chr14:55208170-55386966	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv932970	chr14:55326559-55532749	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv3358123	chr14:55359251-55378030	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
4	esv3345259	chr14:55368427-55370975	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55367000-55370200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr14:55367200-55369800	Active TSS	Liver	Liver
3	chr14:55367400-55369800	Active TSS	GM12878-XiMat	blood
4	chr14:55367600-55369600	Active TSS	Monocytes-CD14+_RO01746	blood
5	chr14:55367600-55370200	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr14:55367600-55370200	Active TSS	Primary T cells from cord blood	blood
7	chr14:55367600-55370200	Active TSS	Right Atrium	heart
8	chr14:55367800-55370000	Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr14:55367800-55370000	Active TSS	Fetal Kidney	kidney
10	chr14:55367800-55370200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr14:55367800-55370200	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr14:55367800-55370200	Active TSS	Colonic Mucosa	Colon
13	chr14:55367800-55370200	Active TSS	Psoas Muscle	Psoas
14	chr14:55367800-55370200	Active TSS	Rectal Smooth Muscle	rectum
15	chr14:55367800-55370200	Active TSS	Right Ventricle	heart
16	chr14:55368000-55369800	Active TSS	Spleen	Spleen
17	chr14:55368000-55370000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr14:55368000-55370000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr14:55368000-55370000	Active TSS	Esophagus	oesophagus
20	chr14:55368000-55370000	Active TSS	Left Ventricle	heart
21	chr14:55368000-55370000	Active TSS	Lung	lung
22	chr14:55368000-55370000	Active TSS	Small Intestine	intestine
23	chr14:55368000-55370200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr14:55368000-55370200	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr14:55368000-55370200	Active TSS	HSMMtube	muscle
26	chr14:55368200-55369800	Active TSS	Primary monocytes fromperipheralblood	blood
27	chr14:55368200-55369800	Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr14:55368200-55369800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr14:55368200-55369800	Active TSS	Brain Angular Gyrus	brain
30	chr14:55368200-55369800	Active TSS	NHEK	skin
31	chr14:55368200-55369800	Active TSS	NHLF	lung
32	chr14:55368200-55370000	Active TSS	Aorta	Aorta
33	chr14:55368200-55370000	Active TSS	Brain Anterior Caudate	brain
34	chr14:55368200-55370000	Active TSS	Gastric	stomach
35	chr14:55368200-55370000	Active TSS	Ovary	ovary
36	chr14:55368200-55370000	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr14:55368200-55370000	Active TSS	Stomach Mucosa	stomach
38	chr14:55368200-55370200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
39	chr14:55368200-55370200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr14:55368200-55370200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr14:55368200-55370200	Active TSS	Duodenum Mucosa	Duodenum
42	chr14:55368200-55370200	Active TSS	Fetal Lung	lung
43	chr14:55368200-55370200	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr14:55368200-55370200	Active TSS	Hela-S3	cervix
45	chr14:55368200-55370200	Active TSS	HSMM	muscle
46	chr14:55368200-55370400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr14:55368400-55369600	Active TSS	Placenta Amnion	Placenta Amnion
48	chr14:55368400-55369800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr14:55368400-55369800	Active TSS	Primary T cells fromperipheralblood	blood
50	chr14:55368400-55369800	Active TSS	Primary T helper naive cells fromperipheralblood	blood

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