Variant report

Variant	rs9897928
Chromosome Location	chr17:59844030-59844031
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59800343..59801227-chr17:59843602..59844157,2	MCF-7	breast:
2	chr17:59488256..59490600-chr17:59842943..59844571,2	MCF-7	breast:
3	chr17:59842148..59844198-chr2:25193933..25196485,2	MCF-7	breast:
4	chr17:59644855..59647910-chr17:59841335..59844150,3	MCF-7	breast:
5	chr17:59820537..59822965-chr17:59841123..59845300,4	MCF-7	breast:
6	chr17:59840941..59844426-chr8:101962904..101965410,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164924	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000115137	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000224165	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1015771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10221278	0.95[CEU][hapmap]
rs10438771	0.95[CEU][hapmap]
rs10468558	0.95[CEU][hapmap]
rs10515206	0.95[CEU][hapmap]
rs10515207	0.89[CEU][hapmap]
rs10515211	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10853038	0.95[CEU][hapmap]
rs11079445	0.95[CEU][hapmap]
rs11650471	0.95[CEU][hapmap]
rs11651510	0.86[EUR][1000 genomes]
rs11653175	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11657480	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11658539	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11871753	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12451862	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs12453293	0.87[EUR][1000 genomes]
rs12453801	0.95[CEU][hapmap]
rs12453935	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs12453966	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs12603617	0.95[CEU][hapmap]
rs12935923	0.84[ASN][1000 genomes]
rs12937232	0.92[EUR][1000 genomes]
rs12948762	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12949659	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12950438	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1468577	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1541346	0.95[CEU][hapmap]
rs1978244	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1990337	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1990338	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2024188	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2040608	0.95[CEU][hapmap]
rs2109252	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2109254	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2109255	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2159450	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2191247	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2191249	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2378884	0.87[EUR][1000 genomes]
rs2378902	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2378905	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2378906	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28571892	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2890012	0.93[CEU][hapmap]
rs2890013	0.95[CEU][hapmap]
rs2890021	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36031690	0.90[EUR][1000 genomes]
rs4309463	0.92[EUR][1000 genomes]
rs4343344	0.92[EUR][1000 genomes]
rs4580256	0.87[EUR][1000 genomes]
rs4968444	0.94[CEU][hapmap]
rs4968447	0.95[CEU][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs4968582	0.95[CEU][hapmap]
rs4988351	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57099937	0.87[EUR][1000 genomes]
rs57393813	0.87[EUR][1000 genomes]
rs62068837	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6504066	0.95[CEU][hapmap]
rs6504068	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6504070	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6504071	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6504072	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs717961	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs717962	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7207074	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs7207881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7208704	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7212172	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7212423	0.94[CEU][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs7213329	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7213470	0.92[EUR][1000 genomes]
rs7213587	0.95[CEU][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs7213759	0.87[EUR][1000 genomes]
rs7214510	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7214884	0.94[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7215784	0.95[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7216011	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7216756	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7216824	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7217206	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7217292	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7220688	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs7220719	0.95[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs7222799	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8074949	0.90[EUR][1000 genomes]
rs8075370	0.95[CEU][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs8075397	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8077088	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8078977	0.89[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8182296	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs9303449	0.95[CEU][hapmap]
rs9807012	0.82[EUR][1000 genomes]
rs9889452	0.82[ASN][1000 genomes]
rs9895987	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9897121	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9897450	0.92[EUR][1000 genomes]
rs9900559	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9902995	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9904292	0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9904294	0.92[EUR][1000 genomes]
rs9905870	0.89[EUR][1000 genomes]
rs9906313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9907299	0.94[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs991378	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[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	esv3427713	chr17:59841820-59844118	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9897928	BRIP1	cis	Nerve Tibial	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59794400-59848200	Weak transcription	HUVEC	blood vessel
2	chr17:59804200-59847400	Weak transcription	K562	blood
3	chr17:59814000-59849000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr17:59815600-59844200	Weak transcription	HMEC	breast
5	chr17:59816800-59887800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr17:59819400-59848200	Weak transcription	Primary B cells from cord blood	blood
7	chr17:59820000-59846600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr17:59820400-59877200	Weak transcription	NH-A	brain
9	chr17:59825800-59846000	Weak transcription	Fetal Intestine Small	intestine
10	chr17:59825800-59898400	Weak transcription	Thymus	Thymus
11	chr17:59827400-59847400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr17:59832000-59846200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr17:59832200-59848400	Weak transcription	HepG2	liver
14	chr17:59835400-59845800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr17:59835800-59848400	Weak transcription	Hela-S3	cervix
16	chr17:59839600-59847000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr17:59839800-59846000	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr17:59839800-59846400	Weak transcription	Fetal Muscle Leg	muscle
19	chr17:59839800-59849000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr17:59840200-59847400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr17:59840200-59848200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr17:59840400-59846000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr17:59840600-59848000	Weak transcription	Fetal Lung	lung
24	chr17:59840600-59848400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr17:59840800-59847200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr17:59840800-59848600	Weak transcription	Fetal Thymus	thymus
27	chr17:59841000-59847400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr17:59841600-59846000	Weak transcription	A549	lung
29	chr17:59841600-59848000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr17:59841600-59856600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:59841800-59845800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr17:59841800-59846000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr17:59842000-59847200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr17:59842000-59848200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr17:59842400-59846200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr17:59842600-59846600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr17:59842600-59847400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:59842600-59848200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr17:59843200-59844600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr17:59843200-59844600	Enhancers	GM12878-XiMat	blood
41	chr17:59843200-59844800	Enhancers	NHDF-Ad	bronchial
42	chr17:59843200-59845000	Enhancers	Osteobl	bone
43	chr17:59843400-59844200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr17:59843400-59844600	Enhancers	NHEK	skin
45	chr17:59843400-59845000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr17:59843600-59844200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr17:59843600-59844200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:59843600-59844200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr17:59843600-59844400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr17:59843600-59844800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links