Variant report

Variant	rs41280120
Chromosome Location	chr17:46114692-46114693
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:122)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:46114231-46114820	MCF-7	breast:	n/a	n/a
2	CTCF	chr17:46113875-46115007	A549	lung:	n/a	n/a
3	CTCF	chr17:46114270-46114709	HepG2	liver:	n/a	n/a
4	CTCF	chr17:46113649-46115069	SK-N-SH	brain:	n/a	n/a
5	MAZ	chr17:46114400-46114843	GM12878	blood:	n/a	n/a
6	POLR2A	chr17:46114223-46115431	ProgFib	skin:	n/a	n/a
7	GABPA	chr17:46114339-46114698	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr17:46114304-46114702	IMR90	lung:	n/a	n/a
9	YY1	chr17:46114351-46114731	A549	lung:	n/a	n/a
10	CTCF	chr17:46114689-46114800	MCF-7	breast:	n/a	n/a
11	JUND	chr17:46114593-46114719	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr17:46114197-46114884	MCF-7	breast:	n/a	n/a
13	POLR2A	chr17:46114392-46114792	A549	lung:	n/a	n/a
14	BACH1	chr17:46114337-46114821	H1-hESC	embryonic stem cell:	n/a	n/a
15	ELF1	chr17:46114235-46114876	GM12878	blood:	n/a	n/a
16	SIN3AK20	chr17:46114632-46115192	PANC-1	pancreas:	n/a	n/a
17	CTCF	chr17:46114282-46114692	H1-hESC	embryonic stem cell:	n/a	n/a
18	JUND	chr17:46114303-46114740	A549	lung:	n/a	n/a
19	TCF12	chr17:46114190-46115023	A549	lung:	n/a	n/a
20	MAX	chr17:46114154-46115029	A549	lung:	n/a	n/a
21	MAX	chr17:46114322-46114698	GM12878	blood:	n/a	n/a
22	RAD21	chr17:46114266-46114696	SK-N-SH_RA	brain:	n/a	chr17:46114673-46114683
23	POLR2A	chr17:46114241-46114932	U87	brain:	n/a	n/a
24	MAX	chr17:46114067-46115700	A549	lung:	n/a	n/a
25	POLR2A	chr17:46114504-46114772	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr17:46114256-46114776	HepG2	liver:	n/a	n/a
27	SIN3AK20	chr17:46114368-46114700	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr17:46114241-46115050	U87	brain:	n/a	n/a
29	RAD21	chr17:46114029-46114759	HepG2	liver:	n/a	chr17:46114673-46114683
30	CREB1	chr17:46114387-46115048	A549	lung:	n/a	n/a
31	POLR2A	chr17:46114578-46114754	HepG2	liver:	n/a	n/a
32	POLR2A	chr17:46114081-46115133	IMR90	lung:	n/a	n/a
33	CTCF	chr17:46114245-46114837	MCF-7	breast:	n/a	n/a
34	MYBL2	chr17:46113974-46114736	HepG2	liver:	n/a	n/a
35	RAD21	chr17:46114230-46114790	H1-hESC	embryonic stem cell:	n/a	chr17:46114673-46114683
36	ELF1	chr17:46114315-46114695	A549	lung:	n/a	n/a
37	CHD2	chr17:46114450-46114846	GM12878	blood:	n/a	n/a
38	CTCF	chr17:46114348-46114769	GM12891	blood:	n/a	n/a
39	CTCF	chr17:46114311-46114791	MCF-7	breast:	n/a	n/a
40	CTCF	chr17:46114292-46114750	A549	lung:	n/a	n/a
41	CTCF	chr17:46114305-46114713	GM12878	blood:	n/a	n/a
42	RAD21	chr17:46114176-46114850	MCF-7	breast:	n/a	chr17:46114673-46114683
43	SIN3AK20	chr17:46114363-46114744	A549	lung:	n/a	n/a
44	RAD21	chr17:46114335-46114895	IMR90	lung:	n/a	chr17:46114673-46114683
45	MYC	chr17:46114270-46114814	MCF-7	breast:	n/a	n/a
46	POLR2A	chr17:46114413-46114701	GM12878	blood:	n/a	n/a
47	SIN3A	chr17:46114327-46115141	H1-hESC	embryonic stem cell:	n/a	chr17:46114983-46114996 chr17:46114682-46114695
48	BCL3	chr17:46114232-46114956	A549	lung:	n/a	chr17:46114501-46114509

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:46114674-46114724	HUVEC	blood vessel:	n/a
2	chr17:46114674-46114724	GM12891	blood:	n/a
3	chr17:46114672-46114722	HCT-116	colon:	n/a
4	chr17:46114674-46114724	HRE	kidney:	n/a
5	chr17:46114674-46114724	AG04450	lung:	fetal
6	chr17:46114674-46114724	PrEC	prostate:	n/a
7	chr17:46114672-46114722	SK-N-MC	brain:	n/a
8	chr17:46114674-46114724	ECC-1	luminal epithelium:	n/a
9	chr17:46114674-46114724	NB4	blood:	n/a
10	chr17:46114672-46114722	IMR90	lung:	fetal
11	chr17:46114674-46114724	HEK293	kidney:	embryo
12	chr17:46114674-46114724	A549	lung:	n/a
13	chr17:46114672-46114722	AG09309	skin:	n/a
14	chr17:46114674-46114724	PFSK-1	brain:	n/a
15	chr17:46114672-46114722	ECC-1	luminal epithelium:	n/a
16	chr17:46114674-46114724	HCM	heart:	n/a
17	chr17:46114672-46114722	HIPEpiC	eye:	n/a
18	chr17:46114674-46114724	HepG2	liver:	n/a
19	chr17:46114672-46114722	NHBE	bronchial:	n/a
20	chr17:46114674-46114724	GM12878	blood:	n/a
21	chr17:46114674-46114724	PANC-1	pancreas:	n/a
22	chr17:46114674-46114724	HRCEpiC	kidney:	n/a
23	chr17:46114674-46114724	T-47D	breast:	n/a
24	chr17:46114672-46114722	NHDF-neo	bronchial:	n/a
25	chr17:46114674-46114724	HPAEpiC	pulmonary alveolar:	n/a
26	chr17:46114674-46114724	MCF-7	breast:	n/a
27	chr17:46114672-46114722	BE2_C	brain:	n/a
28	chr17:46114674-46114724	IMR90	lung:	fetal
29	chr17:46114674-46114724	MCF10A-Er-Src	breast:	n/a
30	chr17:46114674-46114724	SAEC	small airway:	n/a
31	chr17:46114672-46114722	GM19239	blood:	n/a
32	chr17:46114672-46114722	AG10803	skin:	n/a
33	chr17:46114674-46114724	AG10803	skin:	n/a
34	chr17:46114674-46114724	H1-hESC	embryonic stem cell:	embryo
35	chr17:46114674-46114724	HNPCEpiC	eye:	n/a
36	chr17:46114674-46114724	HAEpiC	amniotic membrane:	n/a
37	chr17:46114672-46114722	Hela-S3	cervix:	n/a
38	chr17:46114674-46114724	ProgFib	skin:	n/a
39	chr17:46114674-46114724	Hela-S3	cervix:	n/a
40	chr17:46114674-46114724	GM12892	blood:	n/a
41	chr17:46114672-46114722	MCF-7	breast:	n/a
42	chr17:46114674-46114724	AG09309	skin:	n/a
43	chr17:46114674-46114724	SK-N-SH_RA	brain:	n/a
44	chr17:46114672-46114722	HEEpiC	esophagus:	n/a
45	chr17:46114672-46114722	ProgFib	skin:	n/a
46	chr17:46114674-46114724	NT2-D1	testis:	n/a
47	chr17:46114674-46114724	HCF	heart:	n/a
48	chr17:46114672-46114722	PrEC	prostate:	n/a
49	chr17:46114674-46114724	HEEpiC	esophagus:	n/a
50	chr17:46114674-46114724	GM06990	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46114300..46116159-chr17:46124838..46126678,3	K562	blood:
2	chr16:67063760..67064283-chr17:46114502..46115278,2	MCF-7	breast:

No data

Variant related genes	Relation type
COPZ2	TF binding region
MIR152	TF binding region
MIR152	CpG island
COPZ2	CpG island
ENSG00000263412	Chromatin interaction
ENSG00000067955	Chromatin interaction
ENSG00000082641	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10514938	1.00[ASN][1000 genomes]
rs11650615	1.00[ASN][1000 genomes]
rs16952265	1.00[ASN][1000 genomes]
rs16953235	1.00[ASN][1000 genomes]
rs16953382	1.00[ASN][1000 genomes]
rs16953461	1.00[ASN][1000 genomes]
rs16953925	1.00[ASN][1000 genomes]
rs16954078	1.00[ASN][1000 genomes]
rs16954204	1.00[ASN][1000 genomes]
rs41336845	1.00[ASN][1000 genomes]
rs7216504	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823509	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72823513	0.82[EUR][1000 genomes]
rs72823527	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823530	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823534	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823591	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823592	0.87[EUR][1000 genomes]
rs72823594	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72823599	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823601	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825504	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825512	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825517	1.00[ASN][1000 genomes]
rs72825548	1.00[ASN][1000 genomes]
rs72825584	1.00[ASN][1000 genomes]
rs8067005	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073371	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	esv3427892	chr17:46114053-46116401	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46114000-46114800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr17:46114000-46114800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr17:46114000-46114800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr17:46114000-46114800	Flanking Bivalent TSS/Enh	HepG2	liver
5	chr17:46114000-46115000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:46114000-46115400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr17:46114200-46114800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
8	chr17:46114200-46114800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
9	chr17:46114200-46114800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
10	chr17:46114200-46114800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
11	chr17:46114200-46114800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
12	chr17:46114200-46114800	Flanking Active TSS	NHEK	skin
13	chr17:46114200-46115000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
14	chr17:46114200-46115000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr17:46114200-46115000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr17:46114200-46115000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
17	chr17:46114200-46115000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
18	chr17:46114200-46115000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
19	chr17:46114200-46115000	Flanking Bivalent TSS/Enh	Placenta	Placenta
20	chr17:46114200-46115400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr17:46114200-46115400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr17:46114200-46115400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr17:46114200-46115400	Active TSS	HSMMtube	muscle
24	chr17:46114200-46115600	Active TSS	Fetal Kidney	kidney
25	chr17:46114400-46114800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr17:46114400-46114800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr17:46114400-46114800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr17:46114400-46114800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr17:46114400-46114800	Bivalent/Poised TSS	Primary T helper naive cells from peripheral blood	blood
30	chr17:46114400-46114800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr17:46114400-46114800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr17:46114400-46114800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr17:46114400-46114800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:46114400-46114800	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr17:46114400-46114800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
36	chr17:46114400-46114800	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr17:46114400-46114800	Flanking Active TSS	Ovary	ovary
38	chr17:46114400-46114800	Flanking Active TSS	Pancreas	Pancrea
39	chr17:46114400-46114800	Flanking Bivalent TSS/Enh	Thymus	Thymus
40	chr17:46114400-46114800	Flanking Active TSS	HUVEC	blood vessel
41	chr17:46114400-46115000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
42	chr17:46114400-46115000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
43	chr17:46114400-46115000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
44	chr17:46114400-46115000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
45	chr17:46114400-46115000	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr17:46114400-46115000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
47	chr17:46114400-46115000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr17:46114400-46115000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
49	chr17:46114400-46115000	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
50	chr17:46114400-46115000	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood

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