Variant report

Variant	rs4988340
Chromosome Location	chr17:59940633-59940634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:332)
CpG islands
(count:0)
Chromatin interactive
region (count:47)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:332 , 50 per page) page: 1 2 3 4 5 6 7

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	POLR2A	chr17:59940093-59941287	ECC-1	luminal epithelium:	n/a	n/a
3	MAFF	chr17:59940149-59941418	K562	blood:	n/a	n/a
4	CHD2	chr17:59940314-59941250	GM12878	blood:	n/a	chr17:59940885-59940895
5	USF2	chr17:59940574-59940766	GM12878	blood:	n/a	n/a
6	TBP	chr17:59940246-59941340	H1-hESC	embryonic stem cell:	n/a	n/a
7	YY1	chr17:59940282-59941109	HepG2	liver:	n/a	n/a
8	RCOR1	chr17:59940162-59941415	K562	blood:	n/a	n/a
9	ATF2	chr17:59940337-59941296	GM12878	blood:	n/a	n/a
10	TBP	chr17:59939551-59941842	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr17:59940257-59941266	GM12891	blood:	n/a	n/a
12	ELK1	chr17:59940225-59941237	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr17:59940152-59941522	HCT-116	colon:	n/a	n/a
14	MAX	chr17:59940205-59941166	K562	blood:	n/a	chr17:59940890-59940900
15	YY1	chr17:59940217-59940752	H1-hESC	embryonic stem cell:	n/a	n/a
16	EGR1	chr17:59940502-59941400	HCT-116	colon:	n/a	chr17:59940890-59940903 chr17:59940977-59940990 chr17:59940890-59940903 chr17:59940976-59940991 chr17:59940977-59940990 chr17:59940887-59940901 chr17:59940889-59940904
17	MAX	chr17:59940300-59941173	K562	blood:	n/a	chr17:59940890-59940900
18	SP1	chr17:59940260-59941390	A549	lung:	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
19	POU2F2	chr17:59940633-59940886	GM12878	blood:	n/a	n/a
20	GTF2F1	chr17:59940595-59941223	H1-hESC	embryonic stem cell:	n/a	n/a
21	TEAD4	chr17:59940481-59941491	HepG2	liver:	n/a	n/a
22	POLR2A	chr17:59939567-59941878	Hela-S3	cervix:	n/a	n/a
23	NFATC1	chr17:59940619-59941401	GM12878	blood:	n/a	n/a
24	TAF1	chr17:59940624-59940931	GM12891	blood:	n/a	n/a
25	JUND	chr17:59940430-59941164	A549	lung:	n/a	chr17:59940883-59940892 chr17:59941111-59941123
26	POLR2A	chr17:59940143-59941305	K562	blood:	n/a	n/a
27	POLR2A	chr17:59940581-59941263	HepG2	liver:	n/a	n/a
28	JUND	chr17:59940263-59941583	K562	blood:	n/a	chr17:59940883-59940892 chr17:59941111-59941123
29	KAT2A	chr17:59940171-59941019	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr17:59940201-59941341	HL-60	blood:	n/a	n/a
31	POLR2A	chr17:59940213-59942029	K562	blood:	n/a	n/a
32	GATA3	chr17:59938936-59941431	SK-N-SH	brain:	n/a	chr17:59941286-59941295 chr17:59940695-59940705
33	ZBTB7A	chr17:59940488-59941088	K562	blood:	n/a	chr17:59940981-59940990
34	HEY1	chr17:59940497-59941397	HepG2	liver:	n/a	n/a
35	BRCA1	chr17:59940323-59941199	Hela-S3	cervix:	n/a	n/a
36	RUNX3	chr17:59940414-59941274	GM12878	blood:	n/a	n/a
37	MAX	chr17:59940100-59941410	A549	lung:	n/a	chr17:59940890-59940900
38	POLR2A	chr17:59940204-59941347	GM19193	blood:	n/a	n/a
39	CREB1	chr17:59940360-59941140	A549	lung:	n/a	n/a
40	RFX5	chr17:59938285-59941998	SK-N-SH	brain:	n/a	chr17:59938788-59938796
41	POLR2A	chr17:59940473-59941333	SK-N-MC	brain:	n/a	n/a
42	ZBTB7A	chr17:59940459-59941087	ECC-1	luminal epithelium:	n/a	chr17:59940981-59940990
43	E2F4	chr17:59938928-59941841	MCF10A-Er-Src	breast:	n/a	chr17:59940878-59940889 chr17:59940879-59940891 chr17:59940886-59940898 chr17:59940931-59940940
44	ZNF217	chr17:59938782-59941900	MCF-7	breast:	n/a	n/a
45	FOS	chr17:59940482-59940682	MCF10A-Er-Src	breast:	n/a	n/a
46	BCL3	chr17:59940226-59941562	A549	lung:	n/a	chr17:59940530-59940543
47	POLR2A	chr17:59940284-59941397	MCF-7	breast:	n/a	n/a
48	POLR2A	chr17:59940089-59941382	GM12892	blood:	n/a	n/a
49	STAT5A	chr17:59940504-59940876	GM12878	blood:	n/a	chr17:59940698-59940709
50	TEAD4	chr17:59939000-59941868	A549	lung:	n/a	n/a

No data

(count:47 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:53845723..53846563-chr17:59940443..59941322,2	HCT-116	colon:
2	chr1:121485224..121485933-chr17:59940019..59940634,2	MCF-7	breast:
3	chr1:16840071..16842086-chr17:59939991..59941884,2	MCF-7	breast:
4	chr17:59938126..59942484-chr20:52208111..52210732,4	MCF-7	breast:
5	chr1:173836955..173837586-chr17:59940450..59940985,2	Hela-S3	cervix:
6	chr1:40505868..40506427-chr17:59940412..59941220,2	Hela-S3	cervix:
7	chr17:58160448..58162938-chr17:59938931..59941632,2	MCF-7	breast:
8	chr17:59939694..59942713-chr17:60003159..60007024,4	K562	blood:
9	chr1:154947050..154947598-chr17:59940363..59940949,2	Hela-S3	cervix:
10	chr17:59939732..59941553-chr20:52198983..52200744,2	MCF-7	breast:
11	chr17:59940312..59941187-chr20:55689725..55690292,2	MCF-7	breast:
12	chr14:100842486..100843034-chr17:59940063..59940748,2	Hela-S3	cervix:
13	chr17:59938249..59942766-chr17:60140265..60145745,10	MCF-7	breast:
14	chr17:59940341..59941197-chr21:40177450..40178230,2	Hela-S3	cervix:
15	chr12:112122346..112124894-chr17:59939535..59941780,2	MCF-7	breast:
16	chr1:117602136..117603845-chr17:59938886..59941004,2	MCF-7	breast:
17	chr17:59940451..59941339-chr22:46465320..46465880,2	Hela-S3	cervix:
18	chr17:59939237..59943311-chr20:55795594..55800614,8	MCF-7	breast:
19	chr17:59936074..59944748-chr20:55835834..55847370,36	MCF-7	breast:
20	chr17:59940070..59940863-chr2:165697847..165698683,2	Hela-S3	cervix:
21	chr17:59939253..59942212-chr20:52554185..52557076,2	MCF-7	breast:
22	chr17:59938658..59940749-chr7:99004886..99006495,2	MCF-7	breast:
23	chr17:59940588..59941236-chr9:132388255..132388859,2	MCF-7	breast:
24	chr10:8094609..8097046-chr17:59939983..59942119,2	MCF-7	breast:
25	chr11:61732365..61735270-chr17:59939617..59942181,2	MCF-7	breast:
26	chr17:59939071..59942892-chr17:60002944..60006795,10	MCF-7	breast:
27	chr17:59940465..59941016-chr20:44044742..44045288,2	Hela-S3	cervix:
28	chr17:59936983..59940866-chr17:60141087..60143647,5	MCF-7	breast:
29	chr17:59929026..59944759-chr20:55831267..55853908,71	MCF-7	breast:
30	chr17:59940434..59940965-chr22:39715009..39716000,2	Hela-S3	cervix:
31	chr15:90931064..90931633-chr17:59940294..59940880,2	Hela-S3	cervix:
32	chr17:59476206..59478986-chr17:59937418..59941494,6	MCF-7	breast:
33	chr17:59940588..59942145-chr20:55679663..55681404,2	MCF-7	breast:
34	chr1:27215485..27217208-chr17:59938995..59940925,2	MCF-7	breast:
35	chr17:59939387..59941365-chr20:55678694..55681677,3	MCF-7	breast:
36	chr12:50135021..50135656-chr17:59940406..59941253,2	Hela-S3	cervix:
37	chr17:59939503..59941929-chr8:145689190..145691450,2	MCF-7	breast:
38	chr17:59939694..59942407-chr17:60003159..60006084,4	K562	blood:
39	chr17:59939847..59940652-chr17:60971177..60971870,2	MCF-7	breast:
40	chr17:56707788..56710776-chr17:59939218..59941319,2	MCF-7	breast:
41	chr17:59938976..59941909-chr17:60142630..60144812,2	K562	blood:
42	chr17:59940322..59941206-chr19:39897204..39897809,2	Hela-S3	cervix:
43	chr17:56735014..56738164-chr17:59939669..59942448,4	MCF-7	breast:
44	chr17:59939106..59942463-chr17:60003505..60006582,4	MCF-7	breast:
45	chr17:59940486..59943242-chr17:60081179..60083524,3	MCF-7	breast:
46	chr17:59486255..59492170-chr17:59932286..59941695,13	MCF-7	breast:
47	chr17:59939635..59943027-chr20:55797137..55799971,3	MCF-7	breast:

No data

Variant related genes	Relation type
BRIP1	TF binding region
ENSG00000267131	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000167702	Chromatin interaction
ENSG00000148335	Chromatin interaction
ENSG00000242398	Chromatin interaction
ENSG00000140105	Chromatin interaction
ENSG00000111271	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000108510	Chromatin interaction
ENSG00000203266	Chromatin interaction
ENSG00000261135	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000167996	Chromatin interaction
ENSG00000197111	Chromatin interaction
ENSG00000100316	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000131236	Chromatin interaction
ENSG00000116830	Chromatin interaction
ENSG00000235159	Chromatin interaction
ENSG00000106245	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000107485	Chromatin interaction
ENSG00000108506	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000197308	Chromatin interaction
ENSG00000124155	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000140575	Chromatin interaction
ENSG00000261040	Chromatin interaction
ENSG00000142751	Chromatin interaction
ENSG00000243350	Chromatin interaction
ENSG00000263764	Chromatin interaction
ENSG00000089234	Chromatin interaction
ENSG00000231078	Chromatin interaction
ENSG00000176473	Chromatin interaction
ENSG00000187954	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000173207	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000254578	Chromatin interaction
ENSG00000157557	Chromatin interaction
ENSG00000082438	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12452396	0.87[CEU][hapmap]
rs12602103	0.89[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs12603878	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs12937188	0.81[CHD][hapmap]
rs16945670	0.84[CHB][hapmap]
rs2014444	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6504074	0.89[CEU][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs753765	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs8075585	0.82[ASW][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs8077835	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8081200	0.84[CHB][hapmap];0.91[CHD][hapmap]

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4988340	BRIP1	cis	parietal	SCAN
rs4988340	PTRH2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59938400-59941400	Active TSS	GM12878-XiMat	blood
2	chr17:59938600-59941400	Active TSS	Brain Germinal Matrix	brain
3	chr17:59939000-59941600	Active TSS	H1 Cell Line	embryonic stem cell
4	chr17:59939000-59941600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr17:59939000-59941600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr17:59939200-59941600	Active TSS	Fetal Thymus	thymus
7	chr17:59939200-59941800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr17:59939200-59941800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr17:59939400-59941600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr17:59939400-59941600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr17:59939400-59941600	Active TSS	Fetal Intestine Large	intestine
12	chr17:59939400-59941800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr17:59939400-59941800	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr17:59939400-59941800	Active TSS	Fetal Kidney	kidney
15	chr17:59939600-59941200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr17:59939600-59941200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr17:59939600-59941400	Active TSS	Hela-S3	cervix
18	chr17:59939600-59941600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr17:59939600-59941600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr17:59939600-59941800	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr17:59939800-59941200	Active TSS	NHEK	skin
22	chr17:59939800-59941400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr17:59939800-59941400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr17:59939800-59941400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:59939800-59941600	Active TSS	H9 Cell Line	embryonic stem cell
26	chr17:59939800-59941600	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr17:59939800-59941600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr17:59939800-59941600	Active TSS	Thymus	Thymus
29	chr17:59939800-59941600	Active TSS	NHLF	lung
30	chr17:59939800-59941800	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr17:59939800-59941800	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr17:59940000-59941200	Active TSS	HMEC	breast
33	chr17:59940000-59941200	Active TSS	HSMM	muscle
34	chr17:59940000-59941400	Active TSS	A549	lung
35	chr17:59940000-59941400	Active TSS	Dnd41	blood
36	chr17:59940000-59941600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr17:59940000-59941600	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr17:59940000-59941600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr17:59940000-59941600	Active TSS	K562	blood
40	chr17:59940000-59941600	Active TSS	NH-A	brain
41	chr17:59940000-59941800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr17:59940000-59941800	Active TSS	Fetal Intestine Small	intestine
43	chr17:59940200-59941200	Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr17:59940200-59941200	Active TSS	Brain Cingulate Gyrus	brain
45	chr17:59940200-59941400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr17:59940200-59941400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr17:59940200-59941400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr17:59940200-59941400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr17:59940200-59941400	Active TSS	Brain Angular Gyrus	brain
50	chr17:59940200-59941400	Active TSS	Brain Hippocampus Middle	brain

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