Variant report

Variant	rs66989494
Chromosome Location	chr14:55370121-55370122
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	CTCF	chr14:55370040-55370190	HCT-116	colon:	n/a	chr14:55370049-55370067
2	YY1	chr14:55368649-55370176	HepG2	liver:	n/a	chr14:55368997-55369006 chr14:55368995-55369009 chr14:55368994-55369003 chr14:55368994-55369005
3	CTCF	chr14:55369556-55370208	T-47D	breast:	n/a	chr14:55370049-55370067 chr14:55369674-55369683 chr14:55369671-55369689
4	CREB1	chr14:55368629-55370149	HepG2	liver:	n/a	n/a
5	MAX	chr14:55368526-55370167	Hela-S3	cervix:	n/a	n/a
6	GATA3	chr14:55368282-55370167	MCF-7	breast:	n/a	n/a
7	CREB1	chr14:55369324-55370147	GM12878	blood:	n/a	n/a
8	RAD21	chr14:55369850-55370229	Hela-S3	cervix:	n/a	chr14:55370056-55370065 chr14:55369877-55369889 chr14:55370065-55370077
9	RAD21	chr14:55369452-55370129	HepG2	liver:	n/a	chr14:55370056-55370065 chr14:55369877-55369889 chr14:55370065-55370077
10	CREB1	chr14:55369284-55370176	HepG2	liver:	n/a	n/a
11	RAD21	chr14:55369460-55370207	HepG2	liver:	n/a	chr14:55370056-55370065 chr14:55369877-55369889 chr14:55370065-55370077
12	CTCF	chr14:55369980-55370130	GM12870	blood:	n/a	chr14:55370049-55370067
13	CTCF	chr14:55370000-55370150	SAEC	small airway:	n/a	chr14:55370049-55370067
14	CTCF	chr14:55369349-55370298	K562	blood:	n/a	chr14:55370049-55370067 chr14:55369674-55369683 chr14:55369671-55369689
15	TBP	chr14:55368639-55370148	K562	blood:	n/a	n/a
16	CTCF	chr14:55369577-55370189	MCF-7	breast:	n/a	chr14:55370049-55370067 chr14:55369674-55369683 chr14:55369671-55369689
17	CTCF	chr14:55369508-55370187	GM19238	blood:	n/a	chr14:55370049-55370067 chr14:55369674-55369683 chr14:55369671-55369689
18	CTCF	chr14:55369582-55370184	MCF-7	breast:	n/a	chr14:55370049-55370067 chr14:55369674-55369683 chr14:55369671-55369689
19	CREB1	chr14:55369317-55370131	H1-hESC	embryonic stem cell:	n/a	n/a
20	RAD21	chr14:55369548-55370184	HepG2	liver:	n/a	chr14:55370056-55370065 chr14:55369877-55369889 chr14:55370065-55370077
21	MAX	chr14:55368459-55370154	ECC-1	luminal epithelium:	n/a	n/a
22	CTCF	chr14:55369575-55370172	A549	lung:	n/a	chr14:55370049-55370067 chr14:55369674-55369683 chr14:55369671-55369689
23	TCF7L2	chr14:55368818-55370215	HCT-116	colon:	n/a	chr14:55370156-55370166
24	POLR2A	chr14:55368734-55370227	HepG2	liver:	n/a	n/a
25	PML	chr14:55368680-55370145	MCF-7	breast:	n/a	n/a
26	TFAP2C	chr14:55368557-55370125	Hela-S3	cervix:	n/a	n/a
27	USF2	chr14:55369937-55370193	Hela-S3	cervix:	n/a	n/a
28	MAZ	chr14:55368599-55370174	Hela-S3	cervix:	n/a	n/a
29	NR2F2	chr14:55368519-55370351	MCF-7	breast:	n/a	n/a
30	ZEB1	chr14:55369788-55370170	GM12878	blood:	n/a	n/a
31	ELF1	chr14:55368360-55370452	MCF-7	breast:	n/a	chr14:55369656-55369668
32	CTCF	chr14:55370013-55370137	SK-N-SH_RA	brain:	n/a	chr14:55370049-55370067
33	POLR2A	chr14:55368605-55370294	HepG2	liver:	n/a	n/a
34	CTCF	chr14:55369526-55370207	A549	lung:	n/a	chr14:55370049-55370067 chr14:55369674-55369683 chr14:55369671-55369689
35	CTCF	chr14:55369792-55370163	Pancreas_OC	pancreas:	n/a	chr14:55370049-55370067
36	ZBTB7A	chr14:55369254-55370162	ECC-1	luminal epithelium:	n/a	chr14:55369679-55369688 chr14:55369879-55369888
37	CTCF	chr14:55369597-55370204	T-47D	breast:	n/a	chr14:55370049-55370067 chr14:55369674-55369683 chr14:55369671-55369689
38	CTCF	chr14:55369584-55370149	GM19239	blood:	n/a	chr14:55370049-55370067 chr14:55369674-55369683 chr14:55369671-55369689
39	CTCF	chr14:55369423-55370165	GM12891	blood:	n/a	chr14:55370049-55370067 chr14:55369674-55369683 chr14:55369671-55369689
40	EGR1	chr14:55368440-55370194	HCT-116	colon:	n/a	chr14:55368992-55369005 chr14:55368989-55369003 chr14:55368993-55369002 chr14:55368992-55369005 chr14:55368991-55369006 chr14:55368996-55369006 chr14:55368992-55369005 chr14:55369859-55369869 chr14:55369655-55369669
41	ZEB1	chr14:55368491-55370297	GM12878	blood:	n/a	n/a
42	CTCF	chr14:55369678-55370142	H1-hESC	embryonic stem cell:	n/a	chr14:55370049-55370067
43	CTCF	chr14:55369767-55370164	Hela-S3	cervix:	n/a	chr14:55370049-55370067
44	HDAC2	chr14:55368088-55370292	MCF-7	breast:	n/a	n/a
45	CTCF	chr14:55369541-55370192	K562	blood:	n/a	chr14:55370049-55370067 chr14:55369674-55369683 chr14:55369671-55369689
46	TBP	chr14:55368816-55370166	H1-hESC	embryonic stem cell:	n/a	n/a
47	RAD21	chr14:55369617-55370179	A549	lung:	n/a	chr14:55370056-55370065 chr14:55369877-55369889 chr14:55370065-55370077
48	CTCF	chr14:55370080-55370230	HAc	cerebellar:	n/a	n/a
49	RAD21	chr14:55369717-55370140	H1-hESC	embryonic stem cell:	n/a	chr14:55370056-55370065 chr14:55369877-55369889 chr14:55370065-55370077
50	MAX	chr14:55368337-55370253	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:55368751..55370631-chr14:55518308..55520538,2	K562	blood:
2	chr14:55368311..55371330-chr14:55594542..55598408,4	MCF-7	breast:
3	chr14:55030801..55036234-chr14:55366700..55372024,9	MCF-7	breast:
4	chr14:55343213..55346860-chr14:55368496..55370471,3	MCF-7	breast:
5	chr14:55247890..55252413-chr14:55368163..55370491,5	MCF-7	breast:
6	chr14:55351951..55354870-chr14:55368126..55370512,5	MCF-7	breast:
7	chr14:55367425..55371142-chr14:55516489..55521777,7	MCF-7	breast:
8	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
ENSG00000020577	Chromatin interaction
ENSG00000265432	Chromatin interaction
ENSG00000168175	Chromatin interaction
ENSG00000131981	Chromatin interaction
ENSG00000258872	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10139282	0.83[EUR][1000 genomes]
rs10498471	0.83[EUR][1000 genomes]
rs10873086	0.83[EUR][1000 genomes]
rs11158027	0.83[EUR][1000 genomes]
rs17832281	0.82[AMR][1000 genomes]
rs2183080	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3783637	0.83[EUR][1000 genomes]
rs3783638	0.83[EUR][1000 genomes]
rs3825611	0.83[EUR][1000 genomes]
rs67317740	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs72715545	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73266045	0.82[AMR][1000 genomes]
rs73266060	0.82[AMR][1000 genomes]
rs73266074	0.82[AMR][1000 genomes]
rs8003903	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8004018	0.83[EUR][1000 genomes]
rs8004445	0.83[EUR][1000 genomes]
rs8010461	0.83[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs66989494	GCH1	cis	Whole Blood	GTEx

Chromatin state (count:107 , 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	chr14:55367600-55370200	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr14:55367600-55370200	Active TSS	Primary T cells from cord blood	blood
4	chr14:55367600-55370200	Active TSS	Right Atrium	heart
5	chr14:55367800-55370200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr14:55367800-55370200	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr14:55367800-55370200	Active TSS	Colonic Mucosa	Colon
8	chr14:55367800-55370200	Active TSS	Psoas Muscle	Psoas
9	chr14:55367800-55370200	Active TSS	Rectal Smooth Muscle	rectum
10	chr14:55367800-55370200	Active TSS	Right Ventricle	heart
11	chr14:55368000-55370200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr14:55368000-55370200	Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr14:55368000-55370200	Active TSS	HSMMtube	muscle
14	chr14:55368200-55370200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr14:55368200-55370200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr14:55368200-55370200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr14:55368200-55370200	Active TSS	Duodenum Mucosa	Duodenum
18	chr14:55368200-55370200	Active TSS	Fetal Lung	lung
19	chr14:55368200-55370200	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr14:55368200-55370200	Active TSS	Hela-S3	cervix
21	chr14:55368200-55370200	Active TSS	HSMM	muscle
22	chr14:55368200-55370400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr14:55368400-55370200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
24	chr14:55368400-55370200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr14:55368400-55370200	Active TSS	HMEC	breast
26	chr14:55368600-55370200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr14:55368600-55370200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr14:55368600-55370200	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr14:55368600-55370200	Active TSS	Fetal Heart	heart
30	chr14:55368600-55370200	Active TSS	Fetal Intestine Small	intestine
31	chr14:55368600-55370200	Active TSS	Thymus	Thymus
32	chr14:55368800-55370200	Active TSS	H9 Cell Line	embryonic stem cell
33	chr14:55368800-55370200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:55368800-55370200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr14:55368800-55370200	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr14:55368800-55370200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr14:55368800-55370200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr14:55368800-55370200	Bivalent/Poised TSS	Fetal Brain Female	brain
39	chr14:55368800-55370200	Active TSS	Fetal Intestine Large	intestine
40	chr14:55368800-55370200	Active TSS	NH-A	brain
41	chr14:55368800-55370400	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr14:55369000-55370200	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr14:55369000-55370200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
44	chr14:55369200-55370200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr14:55369400-55370200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr14:55369400-55370200	Active TSS	Primary B cells from cord blood	blood
47	chr14:55369400-55370200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr14:55369600-55370200	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr14:55369600-55370200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr14:55369600-55370200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin

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