Variant report

Variant	rs12940554
Chromosome Location	chr17:46711046-46711047
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr17:46710947-46711048	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr17:46710723-46711397	H1-hESC	embryonic stem cell:	n/a	chr17:46711256-46711266
3	USF1	chr17:46710808-46711097	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr17:46710961-46711402	K562	blood:	n/a	n/a
5	MAX	chr17:46710728-46711215	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTBP2	chr17:46710420-46711534	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr17:46711040-46711190	HFF-Myc	foreskin:	n/a	n/a
8	EGR1	chr17:46711042-46711205	K562	blood:	n/a	chr17:46711146-46711159
9	CTCF	chr17:46711040-46711190	WI-38	lung:	n/a	n/a
10	SUZ12	chr17:46710292-46711548	H1-hESC	embryonic stem cell:	n/a	n/a
11	E2F6	chr17:46710749-46711203	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr17:46708495-46711074	PANC-1	pancreas:	n/a	n/a
13	HMGN3	chr17:46710840-46711323	K562	blood:	n/a	n/a
14	MAX	chr17:46710737-46711195	H1-hESC	embryonic stem cell:	n/a	n/a
15	GABPA	chr17:46710728-46711132	H1-hESC	embryonic stem cell:	n/a	n/a
16	USF1	chr17:46710795-46711167	H1-hESC	embryonic stem cell:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:46711017-46711067	HepG2	liver:	n/a
2	chr17:46711035-46711085	Hepatocyte	liver:	n/a
3	chr17:46711017-46711067	NHBE	bronchial:	n/a
4	chr17:46711017-46711067	PFSK-1	brain:	n/a
5	chr17:46711017-46711067	HCPEpiC	choroid plexus:	n/a
6	chr17:46711017-46711067	Hela-S3	cervix:	n/a
7	chr17:46711035-46711085	SK-N-SH_RA	brain:	n/a
8	chr17:46711035-46711085	PANC-1	pancreas:	n/a
9	chr17:46711035-46711085	AG10803	skin:	n/a
10	chr17:46711035-46711085	NH-A	brain:	n/a
11	chr17:46711035-46711085	PFSK-1	brain:	n/a
12	chr17:46711017-46711067	HCT-116	colon:	n/a
13	chr17:46711035-46711085	BE2_C	brain:	n/a
14	chr17:46711035-46711085	SAEC	small airway:	n/a
15	chr17:46711035-46711085	ProgFib	skin:	n/a
16	chr17:46711017-46711067	HCM	heart:	n/a
17	chr17:46711017-46711067	PrEC	prostate:	n/a
18	chr17:46711035-46711085	Hela-S3	cervix:	n/a
19	chr17:46711017-46711067	SK-N-SH_RA	brain:	n/a
20	chr17:46711035-46711085	HPAEpiC	pulmonary alveolar:	n/a
21	chr17:46711035-46711085	AoSMC	blood vessel:	n/a
22	chr17:46711035-46711085	AG04450	lung:	fetal
23	chr17:46711035-46711085	MCF-7	breast:	n/a
24	chr17:46711017-46711067	NB4	blood:	n/a
25	chr17:46711035-46711085	K562	blood:	n/a
26	chr17:46711035-46711085	A549	lung:	n/a
27	chr17:46711017-46711067	BJ	skin:	n/a
28	chr17:46711017-46711067	IMR90	lung:	fetal
29	chr17:46711017-46711067	BE2_C	brain:	n/a
30	chr17:46711017-46711067	AG04449	skin:	fetal
31	chr17:46711035-46711085	HRPEpiC	eye:	n/a
32	chr17:46711017-46711067	SK-N-MC	brain:	n/a
33	chr17:46711017-46711067	AoSMC	blood vessel:	n/a
34	chr17:46711035-46711085	Caco-2	colon:	n/a
35	chr17:46711035-46711085	HCPEpiC	choroid plexus:	n/a
36	chr17:46711035-46711085	HIPEpiC	eye:	n/a
37	chr17:46711017-46711067	HCF	heart:	n/a
38	chr17:46711035-46711085	HEK293	kidney:	embryo
39	chr17:46711017-46711067	NH-A	brain:	n/a
40	chr17:46711017-46711067	Caco-2	colon:	n/a
41	chr17:46711035-46711085	HUVEC	blood vessel:	n/a
42	chr17:46711017-46711067	RPTEC	kidney:	n/a
43	chr17:46711017-46711067	PANC-1	pancreas:	n/a
44	chr17:46711035-46711085	CMK	blood:	n/a
45	chr17:46711035-46711085	HRCEpiC	kidney:	n/a
46	chr17:46711035-46711085	SK-N-MC	brain:	n/a
47	chr17:46711017-46711067	HMEC	breast:	n/a
48	chr17:46711017-46711067	Jurkat	blood:	n/a
49	chr17:46711017-46711067	MCF10A-Er-Src	breast:	n/a
50	chr17:46711017-46711067	H1-hESC	embryonic stem cell:	embryo

No data

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HOXB7-1	chr17:46710869-46711132	XLOC_012505
2	lnc-HOXB7-1	chr17:46710876-46714135	ENSG00000260027.1

No data

Variant related genes	Relation type
MIR196A1	TF binding region
HOXB7	TF binding region
HOXB7	CpG island
MIR196A1	CpG island

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12952112	1.00[AMR][1000 genomes]
rs34008507	1.00[AMR][1000 genomes]
rs35186512	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35566795	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases
2	nsv908579	chr17:46592413-46727289	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
3	nsv532113	chr17:46598247-47588570	Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	453 gene(s)	inside rSNPs	diseases
4	esv2758459	chr17:46602673-46836837	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
5	esv2758694	chr17:46602673-46836837	Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
6	nsv908581	chr17:46610646-46735520	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
7	nsv833471	chr17:46617787-46783345	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	356 gene(s)	inside rSNPs	diseases
8	nsv908584	chr17:46618926-46735520	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
9	nsv543380	chr17:46686151-46721371	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46708400-46712200	Bivalent/Poised TSS	Colonic Mucosa	Colon
2	chr17:46709600-46712200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
3	chr17:46709800-46711600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr17:46709800-46712200	Weak transcription	A549	lung
5	chr17:46710000-46711200	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
6	chr17:46710000-46711400	Bivalent/Poised TSS	Small Intestine	intestine
7	chr17:46710400-46711200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
8	chr17:46710400-46711200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr17:46710400-46711200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr17:46710600-46711400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr17:46710600-46711600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
12	chr17:46710800-46711200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr17:46710800-46711200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:46710800-46711400	Bivalent Enhancer	Lung	lung
15	chr17:46710800-46711400	Enhancers	Pancreas	Pancrea
16	chr17:46710800-46711400	Bivalent/Poised TSS	HSMM	muscle
17	chr17:46710800-46711600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr17:46710800-46711600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr17:46710800-46711800	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr17:46711000-46711200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr17:46711000-46711200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
22	chr17:46711000-46711200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
23	chr17:46711000-46711200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
24	chr17:46711000-46711200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr17:46711000-46711200	Bivalent Enhancer	Stomach Mucosa	stomach
26	chr17:46711000-46711400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
27	chr17:46711000-46711400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
28	chr17:46711000-46711400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
29	chr17:46711000-46711400	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr17:46711000-46711400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
31	chr17:46711000-46711400	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr17:46711000-46711400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr17:46711000-46711400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:46711000-46711400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
35	chr17:46711000-46711400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr17:46711000-46711400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
37	chr17:46711000-46711600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
38	chr17:46711000-46711600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
39	chr17:46711000-46711600	Bivalent Enhancer	Adipose Nuclei	Adipose
40	chr17:46711000-46711600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr17:46711000-46711600	Bivalent Enhancer	Fetal Muscle Leg	muscle
42	chr17:46711000-46711600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
43	chr17:46711000-46711800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
44	chr17:46711000-46711800	Weak transcription	K562	blood
45	chr17:46711000-46712000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
46	chr17:46711000-46712000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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