Variant report

Variant	rs9900559
Chromosome Location	chr17:59880961-59880962
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59787606..59790047-chr17:59879549..59882493,2	MCF-7	breast:
2	chr1:149818397..149820490-chr17:59879716..59882504,2	MCF-7	breast:
3	chr17:59879426..59881527-chr9:131313572..131315108,2	MCF-7	breast:
4	chr17:59880812..59881395-chr20:57070097..57070655,2	MCF-7	breast:
5	chr17:59810990..59813864-chr17:59880242..59882764,2	MCF-7	breast:
6	chr17:59878729..59881613-chr17:59885443..59887044,2	K562	blood:

Variant related genes	Relation type
ENSG00000197694	Chromatin interaction
ENSG00000228395	Chromatin interaction

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

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

rs_ID	r²[population]
rs1015771	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10515211	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11653175	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11657480	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11658539	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11871753	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12453293	0.80[EUR][1000 genomes]
rs12453935	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12453966	0.80[EUR][1000 genomes]
rs12935923	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12937232	0.84[EUR][1000 genomes]
rs12948762	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12949659	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12950438	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1468577	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978244	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1990337	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1990338	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024188	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2109252	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2109254	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2109255	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2159450	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2191247	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2191249	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2378902	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2378905	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2378906	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28571892	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2890021	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[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	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57099937	0.80[EUR][1000 genomes]
rs57393813	0.80[EUR][1000 genomes]
rs62068837	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6504068	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6504070	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6504071	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6504072	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs717961	0.80[EUR][1000 genomes]
rs7207074	0.80[EUR][1000 genomes]
rs7207881	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7212172	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7212423	0.84[EUR][1000 genomes]
rs7213329	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213470	0.84[EUR][1000 genomes]
rs7213587	0.84[EUR][1000 genomes]
rs7214884	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215784	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7216011	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7216756	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7216824	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217206	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7217292	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7220688	0.80[EUR][1000 genomes]
rs7220719	0.82[EUR][1000 genomes]
rs7222799	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8074949	0.83[EUR][1000 genomes]
rs8075370	0.84[EUR][1000 genomes]
rs8075397	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8077088	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8078977	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8182296	0.80[EUR][1000 genomes]
rs9889452	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9895987	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897121	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897450	0.84[EUR][1000 genomes]
rs9897928	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9902995	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9904292	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9904294	0.84[EUR][1000 genomes]
rs9905870	0.82[EUR][1000 genomes]
rs9906313	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9907299	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs991378	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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
rs9900559	BRIP1	cis	Nerve Tibial	GTEx

Chromatin state (count:54 , 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	chr17:59825800-59898400	Weak transcription	Thymus	Thymus
3	chr17:59844000-59882600	Weak transcription	NHLF	lung
4	chr17:59844600-59882600	Weak transcription	HMEC	breast
5	chr17:59847600-59883400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr17:59848800-59882600	Weak transcription	NHEK	skin
7	chr17:59848800-59911200	Weak transcription	HUVEC	blood vessel
8	chr17:59849400-59887200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr17:59849800-59887200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr17:59850000-59887000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr17:59850000-59887000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr17:59851200-59902600	Weak transcription	Fetal Stomach	stomach
13	chr17:59852600-59898000	Weak transcription	Fetal Intestine Small	intestine
14	chr17:59857000-59888600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:59860200-59883200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:59862000-59887200	Weak transcription	Fetal Kidney	kidney
17	chr17:59863600-59925000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr17:59866000-59883200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr17:59866400-59883400	Weak transcription	Fetal Lung	lung
20	chr17:59867200-59881400	Strong transcription	Dnd41	blood
21	chr17:59868400-59888600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr17:59869200-59898200	Weak transcription	Fetal Muscle Leg	muscle
23	chr17:59869600-59887400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:59870000-59882200	Weak transcription	NHDF-Ad	bronchial
25	chr17:59870400-59933400	Weak transcription	Fetal Intestine Large	intestine
26	chr17:59872000-59882200	Weak transcription	HSMM	muscle
27	chr17:59873000-59882600	Weak transcription	A549	lung
28	chr17:59873200-59905000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr17:59873800-59883400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr17:59874000-59883400	Weak transcription	K562	blood
31	chr17:59874000-59887000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr17:59874400-59910600	Weak transcription	Hela-S3	cervix
33	chr17:59874600-59887200	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr17:59875400-59882600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr17:59875400-59883400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr17:59875400-59886600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr17:59876600-59885600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr17:59876800-59882600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr17:59877000-59882600	Weak transcription	Osteobl	bone
40	chr17:59877600-59882600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr17:59877600-59882600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr17:59878000-59883400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr17:59878200-59881200	Weak transcription	GM12878-XiMat	blood
44	chr17:59878600-59881000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr17:59878800-59882600	Weak transcription	NH-A	brain
46	chr17:59879000-59883000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr17:59879000-59888400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr17:59879400-59898000	Weak transcription	Fetal Thymus	thymus
49	chr17:59879600-59883400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr17:59879600-59893400	Weak transcription	HepG2	liver

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