Variant report

Variant	rs62068837
Chromosome Location	chr17:59888671-59888672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59671815..59673766-chr17:59886224..59888683,2	MCF-7	breast:
2	chr17:59876832..59880358-chr17:59887599..59890424,3	K562	blood:
3	chr17:59887264..59888905-chr17:59890851..59894921,3	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1015771	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10515211	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11653175	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11657480	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11658539	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11871753	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12453293	0.80[EUR][1000 genomes]
rs12453935	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12453966	0.80[EUR][1000 genomes]
rs12935923	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12937232	0.84[EUR][1000 genomes]
rs12948762	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949659	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12950438	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1468577	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1978244	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1990337	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1990338	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2024188	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2109252	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2109254	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2109255	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2159450	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2191247	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2191249	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2378902	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2378905	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2378906	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28571892	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2890021	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36031690	0.83[EUR][1000 genomes]
rs4309463	0.84[EUR][1000 genomes]
rs4343344	0.84[EUR][1000 genomes]
rs4580256	0.80[EUR][1000 genomes]
rs4968447	0.84[EUR][1000 genomes]
rs4988351	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57099937	0.80[EUR][1000 genomes]
rs57393813	0.80[EUR][1000 genomes]
rs6504068	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6504070	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6504071	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6504072	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs717961	0.80[EUR][1000 genomes]
rs7207074	0.80[EUR][1000 genomes]
rs7207881	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7212172	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7212423	0.84[EUR][1000 genomes]
rs7213329	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7213470	0.84[EUR][1000 genomes]
rs7213587	0.84[EUR][1000 genomes]
rs7214884	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7215784	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7216011	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7216756	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7216824	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7217206	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7217292	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7220688	0.80[EUR][1000 genomes]
rs7220719	0.82[EUR][1000 genomes]
rs7222799	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074949	0.83[EUR][1000 genomes]
rs8075370	0.84[EUR][1000 genomes]
rs8075397	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8077088	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078977	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8182296	0.80[EUR][1000 genomes]
rs9889452	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9895987	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9897121	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9897450	0.84[EUR][1000 genomes]
rs9897928	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9900559	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9902995	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9904292	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9904294	0.84[EUR][1000 genomes]
rs9905870	0.82[EUR][1000 genomes]
rs9906313	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9907299	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs991378	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	esv1827960	chr17:59869069-59897455	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
9	nsv575843	chr17:59869081-59935723	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62068837	BRIP1	cis	Nerve Tibial	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59825800-59898400	Weak transcription	Thymus	Thymus
2	chr17:59848800-59911200	Weak transcription	HUVEC	blood vessel
3	chr17:59851200-59902600	Weak transcription	Fetal Stomach	stomach
4	chr17:59852600-59898000	Weak transcription	Fetal Intestine Small	intestine
5	chr17:59863600-59925000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr17:59869200-59898200	Weak transcription	Fetal Muscle Leg	muscle
7	chr17:59870400-59933400	Weak transcription	Fetal Intestine Large	intestine
8	chr17:59873200-59905000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr17:59874400-59910600	Weak transcription	Hela-S3	cervix
10	chr17:59879400-59898000	Weak transcription	Fetal Thymus	thymus
11	chr17:59879600-59893400	Weak transcription	HepG2	liver
12	chr17:59881000-59898400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr17:59882600-59889000	Strong transcription	Dnd41	blood
14	chr17:59883600-59896800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr17:59883600-59898400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:59883800-59893600	Weak transcription	GM12878-XiMat	blood
17	chr17:59883800-59898400	Weak transcription	A549	lung
18	chr17:59884200-59933200	Weak transcription	K562	blood
19	chr17:59884400-59898000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr17:59886200-59893400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr17:59887400-59901600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr17:59887600-59889400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr17:59887600-59893000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr17:59887600-59893400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr17:59887600-59893400	Weak transcription	HMEC	breast
26	chr17:59887600-59893600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr17:59887600-59898200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr17:59887600-59898400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr17:59887600-59899800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr17:59887600-59905200	Weak transcription	Fetal Lung	lung
31	chr17:59887800-59888800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr17:59887800-59891400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr17:59887800-59891600	Weak transcription	Primary B cells from cord blood	blood
34	chr17:59887800-59898000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr17:59887800-59911000	Weak transcription	NH-A	brain
36	chr17:59888000-59889400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr17:59888000-59889600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr17:59888000-59889800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr17:59888000-59890200	Weak transcription	NHDF-Ad	bronchial
40	chr17:59888000-59891600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr17:59888000-59893800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr17:59888000-59898400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr17:59888000-59898400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr17:59888000-59910400	Weak transcription	NHEK	skin
45	chr17:59888000-59911000	Weak transcription	NHLF	lung
46	chr17:59888000-59911400	Weak transcription	HSMM	muscle
47	chr17:59888200-59889400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr17:59888200-59889800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr17:59888400-59889000	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr17:59888600-59889200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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