Variant report

Variant	rs4988351
Chromosome Location	chr17:59857809-59857810
allele	C/G
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	JUND	chr17:59851916-59859108	MCF-7	breast:	n/a	chr17:59852009-59852023 chr17:59857440-59857449
2	GATA3	chr17:59851887-59863123	MCF-7	breast:	n/a	chr17:59857440-59857450 chr17:59861027-59861038
3	ELF1	chr17:59852000-59859117	MCF-7	breast:	n/a	n/a
4	CEBPB	chr17:59851758-59857964	MCF-7	breast:	n/a	chr17:59852026-59852039 chr17:59852027-59852038 chr17:59852028-59852037 chr17:59852028-59852037 chr17:59852026-59852039 chr17:59852028-59852037 chr17:59852884-59852897
5	CTCF	chr17:59857738-59857855	GM10248	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71284384..71284985-chr17:59857688..59858582,2	MCF-7	breast:

Variant related genes	Relation type
BRIP1	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1015771	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10515211	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11653175	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11657480	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11658539	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11871753	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12453293	0.81[EUR][1000 genomes]
rs12453966	0.81[EUR][1000 genomes]
rs12935923	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12937232	0.85[EUR][1000 genomes]
rs12948762	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12949659	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12950438	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1468577	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1978244	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1990337	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1990338	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2024188	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2109252	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2109254	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2109255	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2159450	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2191247	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2191249	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2378884	0.81[EUR][1000 genomes]
rs2378902	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2378905	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2378906	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28571892	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2890021	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36031690	0.84[EUR][1000 genomes]
rs4309463	0.85[EUR][1000 genomes]
rs4343344	0.85[EUR][1000 genomes]
rs4580256	0.81[EUR][1000 genomes]
rs4968447	0.85[EUR][1000 genomes]
rs57099937	0.81[EUR][1000 genomes]
rs57393813	0.81[EUR][1000 genomes]
rs62068837	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6504068	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6504070	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6504071	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6504072	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs717961	0.81[EUR][1000 genomes]
rs7207074	0.81[EUR][1000 genomes]
rs7207881	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7212172	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7212423	0.85[EUR][1000 genomes]
rs7213329	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7213470	0.85[EUR][1000 genomes]
rs7213587	0.85[EUR][1000 genomes]
rs7213759	0.81[EUR][1000 genomes]
rs7214510	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7214884	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7215784	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7216011	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7216756	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7216824	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7217206	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7217292	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7220688	0.81[EUR][1000 genomes]
rs7220719	0.83[EUR][1000 genomes]
rs7222799	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8074949	0.84[EUR][1000 genomes]
rs8075370	0.85[EUR][1000 genomes]
rs8075397	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8077088	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8078977	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8182296	0.81[EUR][1000 genomes]
rs9889452	0.82[ASN][1000 genomes]
rs9895987	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9897121	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9897450	0.85[EUR][1000 genomes]
rs9897928	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9900559	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9902995	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9904292	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9904294	0.85[EUR][1000 genomes]
rs9905870	0.83[EUR][1000 genomes]
rs9906313	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9907299	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs991378	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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	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	nsv908673	chr17:59767501-59926645	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
3	nsv908674	chr17:59800827-59899790	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
4	nsv575841	chr17:59812748-59914681	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv575842	chr17:59812748-59927307	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
6	nsv908675	chr17:59835864-59937286	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4988351	BRIP1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59816800-59887800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr17:59820400-59877200	Weak transcription	NH-A	brain
3	chr17:59825800-59898400	Weak transcription	Thymus	Thymus
4	chr17:59844000-59882600	Weak transcription	NHLF	lung
5	chr17:59844600-59882600	Weak transcription	HMEC	breast
6	chr17:59847600-59883400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr17:59847800-59876200	Weak transcription	Osteobl	bone
8	chr17:59848400-59873600	Weak transcription	K562	blood
9	chr17:59848600-59874000	Weak transcription	Hela-S3	cervix
10	chr17:59848600-59875600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr17:59848800-59872600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr17:59848800-59882600	Weak transcription	NHEK	skin
13	chr17:59848800-59911200	Weak transcription	HUVEC	blood vessel
14	chr17:59849000-59869400	Weak transcription	HepG2	liver
15	chr17:59849400-59871600	Weak transcription	HSMM	muscle
16	chr17:59849400-59872200	Weak transcription	Fetal Thymus	thymus
17	chr17:59849400-59887200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr17:59849800-59858600	Strong transcription	Dnd41	blood
19	chr17:59849800-59887200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr17:59850000-59860400	Weak transcription	GM12878-XiMat	blood
21	chr17:59850000-59865000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr17:59850000-59866000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr17:59850000-59869400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr17:59850000-59870800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr17:59850000-59871000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr17:59850000-59872200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr17:59850000-59873200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr17:59850000-59887000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:59850000-59887000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr17:59851200-59902600	Weak transcription	Fetal Stomach	stomach
31	chr17:59852000-59858600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr17:59852600-59860600	Weak transcription	Primary B cells from cord blood	blood
33	chr17:59852600-59869400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr17:59852600-59898000	Weak transcription	Fetal Intestine Small	intestine
35	chr17:59853800-59869400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr17:59854000-59861600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr17:59854000-59866000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr17:59854000-59868600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr17:59854000-59873000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr17:59856400-59872800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr17:59856800-59858200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr17:59856800-59868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr17:59857000-59888600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr17:59857400-59858200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr17:59857400-59858200	Strong transcription	A549	lung
46	chr17:59857400-59866000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr17:59857600-59858000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr17:59857800-59868200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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