Variant report

Variant	rs6504075
Chromosome Location	chr17:59941540-59941541
allele	G/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	GATA3	chr17:59938482-59942100	MCF-7	breast:	n/a	chr17:59941440-59941447 chr17:59941286-59941295 chr17:59940695-59940705
2	TBP	chr17:59939551-59941842	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr17:59939567-59941878	Hela-S3	cervix:	n/a	n/a
4	JUND	chr17:59940263-59941583	K562	blood:	n/a	chr17:59940883-59940892 chr17:59941111-59941123
5	POLR2A	chr17:59940213-59942029	K562	blood:	n/a	n/a
6	RFX5	chr17:59938285-59941998	SK-N-SH	brain:	n/a	chr17:59938788-59938796
7	E2F4	chr17:59938928-59941841	MCF10A-Er-Src	breast:	n/a	chr17:59940878-59940889 chr17:59940879-59940891 chr17:59940886-59940898 chr17:59940931-59940940
8	ZNF217	chr17:59938782-59941900	MCF-7	breast:	n/a	n/a
9	BCL3	chr17:59940226-59941562	A549	lung:	n/a	chr17:59940530-59940543
10	TEAD4	chr17:59939000-59941868	A549	lung:	n/a	n/a
11	SP1	chr17:59940201-59941551	HCT-116	colon:	n/a	chr17:59940887-59940899 chr17:59940888-59940902 chr17:59940889-59940898 chr17:59940767-59940781 chr17:59940423-59940437 chr17:59940761-59940775 chr17:59940529-59940543 chr17:59940881-59940895 chr17:59940887-59940899
12	SRF	chr17:59938399-59942321	MCF-7	breast:	n/a	chr17:59942006-59942021 chr17:59942008-59942019 chr17:59942009-59942018 chr17:59942007-59942018 chr17:59942005-59942019 chr17:59940890-59940900 chr17:59942009-59942020 chr17:59942005-59942023 chr17:59942007-59942020 chr17:59939748-59939766 chr17:59942005-59942022 chr17:59942008-59942025
13	POLR2A	chr17:59939257-59941574	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr17:59940225-59941583	K562	blood:	n/a	n/a
15	MYC	chr17:59939890-59941579	K562	blood:	n/a	chr17:59940890-59940900
16	IRF1	chr17:59940165-59941690	K562	blood:	n/a	chr17:59940696-59940710 chr17:59941115-59941126 chr17:59940693-59940707 chr17:59940698-59940712 chr17:59940696-59940716 chr17:59941115-59941127 chr17:59941110-59941127 chr17:59940697-59940710 chr17:59940648-59940668
17	ZNF384	chr17:59940477-59941639	GM12878	blood:	n/a	n/a
18	MAFK	chr17:59939553-59941570	K562	blood:	n/a	n/a
19	POLR2A	chr17:59939604-59941754	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr17:59939175-59941694	GM12878	blood:	n/a	n/a
21	HA-E2F1	chr17:59940094-59941573	MCF-7	breast:	n/a	chr17:59940879-59940891 chr17:59940886-59940898 chr17:59940931-59940940 chr17:59940886-59940897
22	IRF1	chr17:59940439-59941681	K562	blood:	n/a	chr17:59940696-59940710 chr17:59941115-59941126 chr17:59940693-59940707 chr17:59940698-59940712 chr17:59940696-59940716 chr17:59941115-59941127 chr17:59941110-59941127 chr17:59940697-59940710 chr17:59940648-59940668
23	POLR2A	chr17:59939300-59941661	Hela-S3	cervix:	n/a	n/a
24	GATA3	chr17:59935970-59945500	MCF-7	breast:	n/a	chr17:59941440-59941447 chr17:59941286-59941295 chr17:59940695-59940705
25	NR2F2	chr17:59938354-59942307	MCF-7	breast:	n/a	n/a
26	POLR2A	chr17:59939034-59941803	GM12891	blood:	n/a	n/a
27	CTCF	chr17:59940904-59941603	K562	blood:	n/a	n/a
28	TAF1	chr17:59940151-59941565	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr17:59940266-59942055	GM12878	blood:	n/a	n/a
30	TBL1XR1	chr17:59940170-59941624	K562	blood:	n/a	n/a
31	POLR2A	chr17:59940287-59941543	PFSK-1	brain:	n/a	n/a
32	ZNF384	chr17:59940313-59941728	K562	blood:	n/a	n/a
33	CCNT2	chr17:59940270-59941688	K562	blood:	n/a	n/a
34	RFX5	chr17:59940217-59941582	Hela-S3	cervix:	n/a	n/a
35	NR2F2	chr17:59937915-59942311	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:59489841..59490368-chr17:59941139..59941856,2	MCF-7	breast:
2	chr1:16840071..16842086-chr17:59939991..59941884,2	MCF-7	breast:
3	chr17:59940889..59941682-chr20:55683508..55684127,2	MCF-7	breast:
4	chr17:59938126..59942484-chr20:52208111..52210732,4	MCF-7	breast:
5	chr17:58160448..58162938-chr17:59938931..59941632,2	MCF-7	breast:
6	chr17:59939694..59942713-chr17:60003159..60007024,4	K562	blood:
7	chr17:59941112..59942997-chr2:20645334..20648313,2	MCF-7	breast:
8	chr17:59939732..59941553-chr20:52198983..52200744,2	MCF-7	breast:
9	chr17:59938249..59942766-chr17:60140265..60145745,10	MCF-7	breast:
10	chr17:59941072..59943147-chr17:61038219..61041304,3	MCF-7	breast:
11	chr12:112122346..112124894-chr17:59939535..59941780,2	MCF-7	breast:
12	chr17:59939237..59943311-chr20:55795594..55800614,8	MCF-7	breast:
13	chr17:59936074..59944748-chr20:55835834..55847370,36	MCF-7	breast:
14	chr17:59939253..59942212-chr20:52554185..52557076,2	MCF-7	breast:
15	chr1:115299174..115301882-chr17:59941089..59942705,2	MCF-7	breast:
16	chr10:8094609..8097046-chr17:59939983..59942119,2	MCF-7	breast:
17	chr11:61732365..61735270-chr17:59939617..59942181,2	MCF-7	breast:
18	chr17:59939071..59942892-chr17:60002944..60006795,10	MCF-7	breast:
19	chr17:59929026..59944759-chr20:55831267..55853908,71	MCF-7	breast:
20	chr17:59940588..59942145-chr20:55679663..55681404,2	MCF-7	breast:
21	chr17:59920538..59922154-chr17:59941018..59942880,2	K562	blood:
22	chr17:59939503..59941929-chr8:145689190..145691450,2	MCF-7	breast:
23	chr17:59939694..59942407-chr17:60003159..60006084,4	K562	blood:
24	chr17:59940965..59941702-chr20:52556109..52557010,2	MCF-7	breast:
25	chr17:59940959..59943336-chr20:52762258..52765062,2	MCF-7	breast:
26	chr17:59938976..59941909-chr17:60142630..60144812,2	K562	blood:
27	chr17:56735014..56738164-chr17:59939669..59942448,4	MCF-7	breast:
28	chr17:59939106..59942463-chr17:60003505..60006582,4	MCF-7	breast:
29	chr17:59940486..59943242-chr17:60081179..60083524,3	MCF-7	breast:
30	chr17:59486255..59492170-chr17:59932286..59941695,13	MCF-7	breast:
31	chr17:59939635..59943027-chr20:55797137..55799971,3	MCF-7	breast:

Variant related genes	Relation type
BRIP1	TF binding region
ENSG00000187954	Chromatin interaction
ENSG00000261135	Chromatin interaction
ENSG00000261040	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000107485	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000254578	Chromatin interaction
ENSG00000167996	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000231078	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000111271	Chromatin interaction
ENSG00000197308	Chromatin interaction
ENSG00000108510	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000089234	Chromatin interaction
ENSG00000242398	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000243350	Chromatin interaction
ENSG00000167702	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000009307	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000108506	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10401014	1.00[EUR][1000 genomes]
rs16945750	1.00[EUR][1000 genomes]
rs28431006	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4988342	0.84[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs58025472	1.00[EUR][1000 genomes]
rs58046635	1.00[EUR][1000 genomes]
rs59794823	1.00[EUR][1000 genomes]
rs6504076	1.00[EUR][1000 genomes]
rs6504078	1.00[EUR][1000 genomes]
rs7211128	1.00[EUR][1000 genomes]
rs7212399	1.00[EUR][1000 genomes]
rs7212824	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7212884	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7213026	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7217530	1.00[EUR][1000 genomes]
rs7221827	1.00[EUR][1000 genomes]
rs7222876	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7224112	1.00[EUR][1000 genomes]
rs7226248	0.84[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs73991952	1.00[EUR][1000 genomes]
rs8065060	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8068267	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs8069386	0.92[ASW][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8069903	1.00[EUR][1000 genomes]
rs8069946	1.00[EUR][1000 genomes]
rs8078342	1.00[EUR][1000 genomes]
rs8081151	0.81[AMR][1000 genomes]
rs9783841	1.00[EUR][1000 genomes]
rs9892063	0.86[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9892123	1.00[EUR][1000 genomes]
rs9894718	0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9896768	1.00[EUR][1000 genomes]
rs9899042	1.00[EUR][1000 genomes]
rs9899780	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9902699	1.00[EUR][1000 genomes]
rs9903562	1.00[EUR][1000 genomes]
rs9905888	1.00[EUR][1000 genomes]
rs9909145	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9909882	0.86[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9910067	1.00[EUR][1000 genomes]
rs9910252	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9910902	1.00[EUR][1000 genomes]
rs9913351	1.00[TSI][hapmap]
rs9914007	1.00[EUR][1000 genomes]
rs9914605	1.00[EUR][1000 genomes]
rs9915023	1.00[EUR][1000 genomes]
rs9916070	1.00[TSI][hapmap]
rs9944467	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59939000-59941600	Active TSS	H1 Cell Line	embryonic stem cell
2	chr17:59939000-59941600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr17:59939000-59941600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr17:59939200-59941600	Active TSS	Fetal Thymus	thymus
5	chr17:59939200-59941800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr17:59939200-59941800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr17:59939400-59941600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:59939400-59941600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr17:59939400-59941600	Active TSS	Fetal Intestine Large	intestine
10	chr17:59939400-59941800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr17:59939400-59941800	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr17:59939400-59941800	Active TSS	Fetal Kidney	kidney
13	chr17:59939600-59941600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr17:59939600-59941600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr17:59939600-59941800	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr17:59939800-59941600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr17:59939800-59941600	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr17:59939800-59941600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr17:59939800-59941600	Active TSS	Thymus	Thymus
20	chr17:59939800-59941600	Active TSS	NHLF	lung
21	chr17:59939800-59941800	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr17:59939800-59941800	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr17:59940000-59941600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr17:59940000-59941600	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr17:59940000-59941600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr17:59940000-59941600	Active TSS	K562	blood
27	chr17:59940000-59941600	Active TSS	NH-A	brain
28	chr17:59940000-59941800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:59940000-59941800	Active TSS	Fetal Intestine Small	intestine
30	chr17:59940200-59941600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr17:59940200-59941600	Active TSS	Primary T cells fromperipheralblood	blood
32	chr17:59940200-59941600	Active TSS	Colonic Mucosa	Colon
33	chr17:59940200-59941600	Active TSS	Esophagus	oesophagus
34	chr17:59940200-59941600	Active TSS	Fetal Brain Male	brain
35	chr17:59940200-59941600	Active TSS	Fetal Muscle Trunk	muscle
36	chr17:59940200-59941600	Active TSS	Placenta	Placenta
37	chr17:59940200-59941600	Active TSS	Ovary	ovary
38	chr17:59940200-59941600	Active TSS	Placenta Amnion	Placenta Amnion
39	chr17:59940200-59941600	Active TSS	Psoas Muscle	Psoas
40	chr17:59940200-59941600	Active TSS	Right Atrium	heart
41	chr17:59940200-59941600	Active TSS	Right Ventricle	heart
42	chr17:59940200-59941600	Active TSS	HSMMtube	muscle
43	chr17:59940200-59941800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr17:59940200-59941800	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr17:59940200-59941800	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr17:59940200-59941800	Active TSS	Rectal Smooth Muscle	rectum
47	chr17:59940400-59941600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr17:59940400-59941600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr17:59940400-59941600	Active TSS	Brain Substantia Nigra	brain
50	chr17:59940400-59941600	Active TSS	Fetal Adrenal Gland	Adrenal Gland

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