Variant report

Variant	rs12935923
Chromosome Location	chr17:59867775-59867776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59866718..59868702-chr17:59911534..59913402,2	MCF-7	breast:
2	chr17:59867062..59867822-chr17:59895146..59895863,2	MCF-7	breast:
3	chr1:115210634..115212515-chr17:59866930..59869846,2	MCF-7	breast:
4	chr17:59867134..59868670-chr20:52610022..52612203,2	MCF-7	breast:
5	chr17:59867365..59870149-chr20:52184206..52185807,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1015771	0.83[ASN][1000 genomes]
rs10515211	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11653175	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11657480	0.80[AMR][1000 genomes]
rs11658539	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11871753	0.83[ASN][1000 genomes]
rs12948762	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12949659	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12950438	0.83[ASN][1000 genomes]
rs1468577	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1978244	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1990337	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1990338	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2378902	0.83[ASN][1000 genomes]
rs2378905	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2378906	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28571892	0.83[ASN][1000 genomes]
rs4988351	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62068837	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6504070	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6504071	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6504072	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7207881	0.83[ASN][1000 genomes]
rs7212172	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7213329	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7214884	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7215784	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7216011	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7216756	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7216824	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7217206	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7222799	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8077088	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8078977	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9889452	0.83[AMR][1000 genomes]
rs9895987	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9897121	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9897928	0.84[ASN][1000 genomes]
rs9900559	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9904292	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9906313	0.83[ASN][1000 genomes]
rs9907299	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs991378	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	esv1794309	chr17:59861640-59907952	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12935923	BRIP1	cis	Nerve Tibial	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

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	chr17:59849800-59887200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr17:59850000-59869400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr17:59850000-59870800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr17:59850000-59871000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr17:59850000-59872200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr17:59850000-59873200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr17:59850000-59887000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr17:59850000-59887000	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr17:59851200-59902600	Weak transcription	Fetal Stomach	stomach
27	chr17:59852600-59869400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr17:59852600-59898000	Weak transcription	Fetal Intestine Small	intestine
29	chr17:59853800-59869400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr17:59854000-59868600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr17:59854000-59873000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr17:59856400-59872800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr17:59856800-59868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr17:59857000-59888600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:59857800-59868200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr17:59858000-59872800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr17:59858200-59869400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr17:59860200-59883200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:59860800-59868000	Weak transcription	A549	lung
40	chr17:59862000-59869200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr17:59862000-59887200	Weak transcription	Fetal Kidney	kidney
42	chr17:59863200-59869800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr17:59863600-59925000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr17:59863800-59876200	Weak transcription	GM12878-XiMat	blood
45	chr17:59864000-59871200	Weak transcription	Primary B cells from cord blood	blood
46	chr17:59865400-59873800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr17:59866000-59880800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr17:59866000-59883200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr17:59866200-59869800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr17:59866400-59883400	Weak transcription	Fetal Lung	lung

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