Variant report

Variant	rs2109252
Chromosome Location	chr17:59828811-59828812
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1015771	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10515211	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11651510	0.85[EUR][1000 genomes]
rs11653175	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11657480	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11658539	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11871753	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12451862	0.85[EUR][1000 genomes]
rs12453293	0.87[EUR][1000 genomes]
rs12453966	0.87[EUR][1000 genomes]
rs12937232	0.91[EUR][1000 genomes]
rs12948762	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12949659	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12950438	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1468577	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1978244	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1990337	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1990338	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2024188	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109255	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2191247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2191249	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2378884	0.86[EUR][1000 genomes]
rs2378902	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2378905	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2378906	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28571892	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2890021	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36031690	0.90[EUR][1000 genomes]
rs4309463	0.91[EUR][1000 genomes]
rs4343344	0.91[EUR][1000 genomes]
rs4580256	0.87[EUR][1000 genomes]
rs4968447	0.91[EUR][1000 genomes]
rs4988351	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57099937	0.87[EUR][1000 genomes]
rs57393813	0.87[EUR][1000 genomes]
rs62068837	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6504068	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6504070	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6504071	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6504072	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs717961	0.87[EUR][1000 genomes]
rs717962	0.85[EUR][1000 genomes]
rs7207074	0.87[EUR][1000 genomes]
rs7207881	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7212172	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7212423	0.91[EUR][1000 genomes]
rs7213329	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7213470	0.91[EUR][1000 genomes]
rs7213587	0.91[EUR][1000 genomes]
rs7213759	0.86[EUR][1000 genomes]
rs7214884	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7215784	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7216011	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7216756	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7216824	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7217206	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7217292	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7220688	0.87[EUR][1000 genomes]
rs7220719	0.89[EUR][1000 genomes]
rs7222799	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8074949	0.90[EUR][1000 genomes]
rs8075370	0.91[EUR][1000 genomes]
rs8075397	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8077088	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8078977	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8182296	0.87[EUR][1000 genomes]
rs9807012	0.82[EUR][1000 genomes]
rs9895987	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9897121	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9897450	0.91[EUR][1000 genomes]
rs9897928	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9900559	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9902995	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9904292	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9904294	0.91[EUR][1000 genomes]
rs9905870	0.88[EUR][1000 genomes]
rs9906313	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9907299	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs991378	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2109252	BRIP1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59781600-59835400	Weak transcription	Hela-S3	cervix
2	chr17:59794400-59848200	Weak transcription	HUVEC	blood vessel
3	chr17:59804200-59847400	Weak transcription	K562	blood
4	chr17:59804600-59834200	Weak transcription	Osteobl	bone
5	chr17:59807600-59838400	Weak transcription	Fetal Stomach	stomach
6	chr17:59814000-59849000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr17:59815000-59839200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr17:59815600-59836000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr17:59815600-59844200	Weak transcription	HMEC	breast
10	chr17:59815800-59834400	Weak transcription	HSMM	muscle
11	chr17:59815800-59843400	Weak transcription	NHEK	skin
12	chr17:59816800-59887800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr17:59819000-59842600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr17:59819400-59843600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr17:59819400-59848200	Weak transcription	Primary B cells from cord blood	blood
16	chr17:59820000-59839200	Weak transcription	Fetal Muscle Leg	muscle
17	chr17:59820000-59841400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:59820000-59841400	Weak transcription	Ovary	ovary
19	chr17:59820000-59846600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr17:59820400-59835400	Weak transcription	Fetal Intestine Large	intestine
21	chr17:59820400-59840200	Weak transcription	Fetal Thymus	thymus
22	chr17:59820400-59877200	Weak transcription	NH-A	brain
23	chr17:59821400-59831600	Weak transcription	HepG2	liver
24	chr17:59821400-59834200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr17:59824400-59831800	Weak transcription	Primary T cells from cord blood	blood
26	chr17:59824400-59832000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr17:59824400-59839200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr17:59825000-59840000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr17:59825600-59829000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr17:59825600-59834600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr17:59825800-59831000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr17:59825800-59838600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr17:59825800-59846000	Weak transcription	Fetal Intestine Small	intestine
34	chr17:59825800-59898400	Weak transcription	Thymus	Thymus
35	chr17:59826000-59831400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr17:59826000-59839400	Weak transcription	Fetal Lung	lung
37	chr17:59826000-59841400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr17:59826200-59830200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr17:59826200-59830400	Weak transcription	A549	lung
40	chr17:59826200-59839600	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr17:59827000-59830200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr17:59827000-59834400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr17:59827000-59839600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr17:59827400-59847400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr17:59827600-59830200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr17:59827600-59835600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr17:59827600-59835800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr17:59827600-59839200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr17:59827600-59839200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr17:59828200-59840200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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