Variant report

Variant	rs2012954
Chromosome Location	chr17:17184399-17184400
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:401)
CpG islands
(count:61)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:401 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr17:17183697-17185174	A549	lung:	n/a	n/a
2	USF1	chr17:17183916-17184803	ECC-1	luminal epithelium:	n/a	chr17:17184207-17184223
3	PML	chr17:17184198-17184929	K562	blood:	n/a	n/a
4	SP2	chr17:17183824-17184571	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr17:17183806-17184937	GM12892	blood:	n/a	n/a
6	CHD2	chr17:17183906-17185110	K562	blood:	n/a	chr17:17184198-17184208
7	ATF1	chr17:17183975-17184885	K562	blood:	n/a	n/a
8	NR3C1	chr17:17184357-17184800	A549	lung:	n/a	n/a
9	HA-E2F1	chr17:17183649-17184940	MCF-7	breast:	n/a	chr17:17184536-17184547
10	NFATC1	chr17:17184364-17184852	GM12878	blood:	n/a	chr17:17184665-17184678
11	ATF3	chr17:17184179-17184932	A549	lung:	n/a	n/a
12	POLR2A	chr17:17183803-17185007	ECC-1	luminal epithelium:	n/a	n/a
13	EP300	chr17:17183904-17184940	GM12878	blood:	n/a	chr17:17184216-17184232
14	ZBTB33	chr17:17184358-17184901	GM12878	blood:	n/a	chr17:17184591-17184601 chr17:17184588-17184603
15	TBP	chr17:17183919-17184991	Hela-S3	cervix:	n/a	n/a
16	GATA3	chr17:17183800-17185157	A549	lung:	n/a	n/a
17	POLR2A	chr17:17183862-17185070	GM12878	blood:	n/a	n/a
18	JUND	chr17:17183933-17184913	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr17:17183891-17184785	Hela-S3	cervix:	n/a	chr17:17184192-17184202 chr17:17184665-17184674 chr17:17184669-17184678
20	SIN3AK20	chr17:17184015-17184881	PFSK-1	brain:	n/a	n/a
21	TAF7	chr17:17184248-17184687	H1-hESC	embryonic stem cell:	n/a	n/a
22	YY1	chr17:17184296-17184688	K562	blood:	n/a	chr17:17184570-17184579 chr17:17184568-17184579
23	POLR2A	chr17:17183872-17184867	Hela-S3	cervix:	n/a	n/a
24	ETS1	chr17:17183804-17184966	A549	lung:	n/a	chr17:17184133-17184149 chr17:17184611-17184620 chr17:17184197-17184208 chr17:17184609-17184619
25	GABPA	chr17:17183738-17184757	K562	blood:	n/a	n/a
26	KAP1	chr17:17184337-17185257	U2OS	brain:	n/a	n/a
27	E2F6	chr17:17183997-17184739	K562	blood:	n/a	chr17:17184537-17184548
28	POLR2A	chr17:17183720-17185169	H1-hESC	embryonic stem cell:	n/a	n/a
29	ELF1	chr17:17184345-17185113	A549	lung:	n/a	chr17:17184692-17184705
30	TAF1	chr17:17183837-17184868	K562	blood:	n/a	n/a
31	POLR2A	chr17:17183805-17184951	GM19099	blood:	n/a	n/a
32	PBX3	chr17:17183817-17185002	SK-N-SH	brain:	n/a	n/a
33	HEY1	chr17:17183806-17184795	HepG2	liver:	n/a	n/a
34	SIN3AK20	chr17:17184378-17184818	HepG2	liver:	n/a	n/a
35	YY1	chr17:17183832-17184725	HepG2	liver:	n/a	chr17:17184570-17184579 chr17:17184568-17184579
36	E2F6	chr17:17184074-17184853	H1-hESC	embryonic stem cell:	n/a	chr17:17184537-17184548
37	ZEB1	chr17:17184024-17184637	GM12878	blood:	n/a	n/a
38	IRF1	chr17:17183932-17184974	K562	blood:	n/a	chr17:17184144-17184158
39	POLR2A	chr17:17184323-17184944	SK-N-SH	brain:	n/a	n/a
40	GABPA	chr17:17183877-17184883	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr17:17183803-17185095	NB4	blood:	n/a	n/a
42	MAX	chr17:17183764-17184965	ECC-1	luminal epithelium:	n/a	chr17:17184192-17184202 chr17:17184665-17184674 chr17:17184669-17184678
43	SP1	chr17:17183810-17184830	H1-hESC	embryonic stem cell:	n/a	chr17:17184195-17184209 chr17:17184561-17184573 chr17:17184198-17184210 chr17:17184198-17184210 chr17:17184199-17184208
44	CHD2	chr17:17183856-17184978	GM12878	blood:	n/a	chr17:17184198-17184208
45	TCF12	chr17:17183700-17185248	A549	lung:	n/a	n/a
46	MAFK	chr17:17183931-17185006	Hela-S3	cervix:	n/a	chr17:17184034-17184049 chr17:17184034-17184050
47	POU2F2	chr17:17184289-17184863	GM12891	blood:	n/a	n/a
48	TCF7L2	chr17:17184017-17184633	PANC-1	pancreas:	n/a	n/a
49	CREB1	chr17:17184347-17184930	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr17:17183723-17185127	U87	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:17184369-17184419	NH-A	brain:	n/a
2	chr17:17184369-17184419	HCPEpiC	choroid plexus:	n/a
3	chr17:17184369-17184419	Hela-S3	cervix:	n/a
4	chr17:17184369-17184419	GM12891	blood:	n/a
5	chr17:17184369-17184419	HEEpiC	esophagus:	n/a
6	chr17:17184369-17184419	HRCEpiC	kidney:	n/a
7	chr17:17184369-17184419	PrEC	prostate:	n/a
8	chr17:17184369-17184419	ProgFib	skin:	n/a
9	chr17:17184369-17184419	ovcar-3	ovarian:	n/a
10	chr17:17184369-17184419	Jurkat	blood:	n/a
11	chr17:17184369-17184419	HEK293	kidney:	embryo
12	chr17:17184369-17184419	U87	brain:	n/a
13	chr17:17184369-17184419	IMR90	lung:	fetal
14	chr17:17184369-17184419	SKMC	muscle:	n/a
15	chr17:17184369-17184419	SK-N-MC	brain:	n/a
16	chr17:17184369-17184419	MCF-7	breast:	n/a
17	chr17:17184369-17184419	SK-N-SH	brain:	n/a
18	chr17:17184369-17184419	RPTEC	kidney:	n/a
19	chr17:17184369-17184419	HMEC	breast:	n/a
20	chr17:17184369-17184419	NHBE	bronchial:	n/a
21	chr17:17184369-17184419	HUVEC	blood vessel:	n/a
22	chr17:17184369-17184419	HAEpiC	amniotic membrane:	n/a
23	chr17:17184369-17184419	MCF10A-Er-Src	breast:	n/a
24	chr17:17184369-17184419	CMK	blood:	n/a
25	chr17:17184369-17184419	HIPEpiC	eye:	n/a
26	chr17:17184369-17184419	PANC-1	pancreas:	n/a
27	chr17:17184369-17184419	NT2-D1	testis:	n/a
28	chr17:17184369-17184419	H1-hESC	embryonic stem cell:	embryo
29	chr17:17184369-17184419	HepG2	liver:	n/a
30	chr17:17184369-17184419	LNCaP	prostate:	n/a
31	chr17:17184369-17184419	HRPEpiC	eye:	n/a
32	chr17:17184369-17184419	Hepatocyte	liver:	n/a
33	chr17:17184369-17184419	GM12878	blood:	n/a
34	chr17:17184369-17184419	AG09319	gingival:	n/a
35	chr17:17184369-17184419	HCM	heart:	n/a
36	chr17:17184369-17184419	PFSK-1	brain:	n/a
37	chr17:17184369-17184419	GM19239	blood:	n/a
38	chr17:17184369-17184419	ECC-1	luminal epithelium:	n/a
39	chr17:17184369-17184419	HNPCEpiC	eye:	n/a
40	chr17:17184369-17184419	AG04449	skin:	fetal
41	chr17:17184369-17184419	GM06990	blood:	n/a
42	chr17:17184369-17184419	BE2_C	brain:	n/a
43	chr17:17184369-17184419	HCT-116	colon:	n/a
44	chr17:17184369-17184419	AG09309	skin:	n/a
45	chr17:17184369-17184419	SAEC	small airway:	n/a
46	chr17:17184369-17184419	SK-N-SH_RA	brain:	n/a
47	chr17:17184369-17184419	T-47D	breast:	n/a
48	chr17:17184369-17184419	BJ	skin:	n/a
49	chr17:17184369-17184419	GM12892	blood:	n/a
50	chr17:17184369-17184419	HL-60	blood:	n/a

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17177648..17180936-chr17:17181197..17184729,6	MCF-7	breast:
2	chr11:62609146..62609719-chr17:17184144..17184739,2	NB4	blood:
3	chr17:17182421..17186483-chr17:17204152..17209830,5	MCF-7	breast:
4	chr1:92763984..92764912-chr17:17184143..17184722,2	Hela-S3	cervix:
5	chr15:65596820..65597667-chr17:17184161..17184674,2	Hela-S3	cervix:
6	chr17:17138280..17141930-chr17:17183181..17187644,4	MCF-7	breast:
7	chr17:17139508..17142367-chr17:17182538..17186121,3	MCF-7	breast:
8	chr17:17183415..17186229-chr17:17206165..17209020,3	MCF-7	breast:
9	chr17:17138181..17140588-chr17:17182569..17184810,2	K562	blood:
10	chr17:17183059..17186537-chr17:17204352..17209458,5	K562	blood:
11	chr1:225117293..225117949-chr17:17184296..17185001,2	Hela-S3	cervix:
12	chr17:17132573..17135085-chr17:17184051..17185920,2	K562	blood:
13	chr17:17181690..17186423-chr17:17204352..17210529,13	K562	blood:
14	chr14:60558608..60559155-chr17:17184009..17184723,2	Hela-S3	cervix:
15	chr17:17173847..17176636-chr17:17182577..17185189,4	MCF-7	breast:

No data

Variant related genes	Relation type
COPS3	TF binding region
COPS3	CpG island
ENSG00000200156	Chromatin interaction
ENSG00000264187	Chromatin interaction
ENSG00000205309	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000154803	Chromatin interaction
ENSG00000185842	Chromatin interaction
ENSG00000141030	Chromatin interaction
ENSG00000126773	Chromatin interaction
ENSG00000122484	Chromatin interaction
ENSG00000266498	Chromatin interaction
ENSG00000174842	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12453455	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12600589	0.92[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs1630656	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1708617	0.92[ASN][1000 genomes]
rs1708621	0.92[ASN][1000 genomes]
rs1708624	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1708625	0.83[EUR][1000 genomes]
rs1708628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1736204	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1736205	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1736208	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.94[ASN][1000 genomes]
rs1736209	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs1736211	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.92[ASN][1000 genomes]
rs1736212	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs1736216	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs1736217	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs1736221	0.90[ASN][1000 genomes]
rs2018781	0.92[ASN][1000 genomes]
rs2292527	0.92[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2472689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36079048	0.88[ASN][1000 genomes]
rs3866959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62066065	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62066066	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6502564	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs6502568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502571	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7217560	0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7220577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7220827	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs7221553	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224598	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7225876	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8066090	0.92[ASN][1000 genomes]
rs8080386	0.92[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9892352	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9894565	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833380	chr17:17088416-17241206	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1065811	chr17:17104760-17225204	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv833382	chr17:17124329-17305683	Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv469777	chr17:17127385-17272698	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv482546	chr17:17127385-17272698	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv9499	chr17:17181611-17187670	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17182800-17185000	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr17:17182800-17185000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr17:17183000-17184800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr17:17183000-17185200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr17:17183200-17184800	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr17:17183200-17184800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr17:17183200-17184800	Active TSS	K562	blood
8	chr17:17183200-17185000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr17:17183200-17185000	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr17:17183200-17185000	Active TSS	NHDF-Ad	bronchial
11	chr17:17183200-17185200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr17:17183200-17185200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr17:17183200-17185200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr17:17183200-17185200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr17:17183200-17185400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:17183200-17185400	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr17:17183200-17185400	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr17:17183400-17184400	Active TSS	HepG2	liver
19	chr17:17183400-17184600	Weak transcription	Fetal Heart	heart
20	chr17:17183400-17184600	Active TSS	Small Intestine	intestine
21	chr17:17183400-17184600	Active TSS	HSMM	muscle
22	chr17:17183400-17184800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:17183400-17184800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr17:17183400-17184800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr17:17183400-17184800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr17:17183400-17184800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr17:17183400-17184800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr17:17183400-17184800	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr17:17183400-17184800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr17:17183400-17184800	Active TSS	Brain Hippocampus Middle	brain
31	chr17:17183400-17184800	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr17:17183400-17184800	Active TSS	Brain Substantia Nigra	brain
33	chr17:17183400-17184800	Active TSS	Colon Smooth Muscle	Colon
34	chr17:17183400-17184800	Active TSS	Fetal Lung	lung
35	chr17:17183400-17184800	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr17:17183400-17184800	Active TSS	Rectal Smooth Muscle	rectum
37	chr17:17183400-17184800	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr17:17183400-17184800	Active TSS	A549	lung
39	chr17:17183400-17184800	Active TSS	Dnd41	blood
40	chr17:17183400-17184800	Active TSS	GM12878-XiMat	blood
41	chr17:17183400-17184800	Active TSS	Hela-S3	cervix
42	chr17:17183400-17184800	Active TSS	HMEC	breast
43	chr17:17183400-17184800	Active TSS	HSMMtube	muscle
44	chr17:17183400-17184800	Active TSS	NH-A	brain
45	chr17:17183400-17184800	Active TSS	NHEK	skin
46	chr17:17183400-17184800	Active TSS	NHLF	lung
47	chr17:17183400-17185000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr17:17183400-17185000	Active TSS	Duodenum Mucosa	Duodenum
49	chr17:17183400-17185000	Active TSS	Esophagus	oesophagus
50	chr17:17183400-17185000	Active TSS	Fetal Intestine Large	intestine

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