Variant report

Variant	rs9907299
Chromosome Location	chr17:59886992-59886993
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59878729..59881613-chr17:59885443..59887044,2	K562	blood:
2	chr17:57912982..57915628-chr17:59885852..59887538,2	MCF-7	breast:
3	chr17:59671815..59673766-chr17:59886224..59888683,2	MCF-7	breast:
4	chr17:59885614..59888550-chr20:55780015..55782041,2	MCF-7	breast:
5	chr17:59885837..59887691-chr17:59940605..59942107,2	MCF-7	breast:
6	chr1:214818661..214820186-chr17:59886646..59888355,2	MCF-7	breast:
7	chr17:59773260..59775914-chr17:59885795..59887356,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136492	Chromatin interaction
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1015771	0.94[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10221278	0.89[CEU][hapmap]
rs10438771	0.89[CEU][hapmap]
rs10468558	0.89[CEU][hapmap]
rs10515206	0.89[CEU][hapmap]
rs10515207	0.82[CEU][hapmap]
rs10515211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10853038	0.89[CEU][hapmap]
rs11079445	0.89[CEU][hapmap]
rs11650471	0.89[CEU][hapmap]
rs11653175	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11657480	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11658539	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11871753	0.89[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12451862	0.89[CEU][hapmap]
rs12453293	0.80[EUR][1000 genomes]
rs12453801	0.89[CEU][hapmap]
rs12453935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12453966	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs12603617	0.89[CEU][hapmap]
rs12935923	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12937232	0.84[EUR][1000 genomes]
rs12948762	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12949659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12950438	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1468577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541346	0.89[CEU][hapmap]
rs1978244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1990337	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1990338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024188	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2040608	0.89[CEU][hapmap]
rs2109252	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2109254	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2109255	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2159450	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2191247	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2191249	0.94[CEU][hapmap];0.86[CHB][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2378902	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2378905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2378906	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28571892	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2890012	0.85[CEU][hapmap]
rs2890013	0.89[CEU][hapmap]
rs2890021	0.95[CEU][hapmap];0.86[CHB][hapmap];0.80[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]
rs4968444	0.89[CEU][hapmap]
rs4968447	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs4968582	0.89[CEU][hapmap]
rs4988351	0.85[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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6504066	0.89[CEU][hapmap]
rs6504068	0.94[CEU][hapmap];0.85[CHB][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6504070	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6504071	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6504072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs717961	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs717962	0.89[CEU][hapmap]
rs7207074	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7207881	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7208704	0.94[CEU][hapmap];0.93[JPT][hapmap]
rs7212172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7212423	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs7213329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213470	0.84[EUR][1000 genomes]
rs7213587	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs7214884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7216011	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7216756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7216824	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7217292	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7220688	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7220719	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7222799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8074949	0.83[EUR][1000 genomes]
rs8075370	0.89[CEU][hapmap];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];0.98[ASN][1000 genomes]
rs8078977	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8182296	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs9303449	0.89[CEU][hapmap]
rs9889452	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9895987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897450	0.84[EUR][1000 genomes]
rs9897928	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]
rs9900559	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9902995	0.94[CEU][hapmap];0.86[CHB][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9904292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[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	0.94[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs991378	0.83[AFR][1000 genomes];1.00[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
rs9907299	BRIP1	cis	Nerve Tibial	GTEx

Chromatin state (count:61 , 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	chr17:59848800-59911200	Weak transcription	HUVEC	blood vessel
4	chr17:59849400-59887200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr17:59849800-59887200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr17:59850000-59887000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr17:59850000-59887000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr17:59851200-59902600	Weak transcription	Fetal Stomach	stomach
9	chr17:59852600-59898000	Weak transcription	Fetal Intestine Small	intestine
10	chr17:59857000-59888600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:59862000-59887200	Weak transcription	Fetal Kidney	kidney
12	chr17:59863600-59925000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr17:59868400-59888600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr17:59869200-59898200	Weak transcription	Fetal Muscle Leg	muscle
15	chr17:59869600-59887400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr17:59870400-59933400	Weak transcription	Fetal Intestine Large	intestine
17	chr17:59873200-59905000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr17:59874000-59887000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr17:59874400-59910600	Weak transcription	Hela-S3	cervix
20	chr17:59874600-59887200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr17:59879000-59888400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr17:59879400-59898000	Weak transcription	Fetal Thymus	thymus
23	chr17:59879600-59893400	Weak transcription	HepG2	liver
24	chr17:59880800-59887200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr17:59881000-59898400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr17:59882600-59889000	Strong transcription	Dnd41	blood
27	chr17:59883000-59887200	Weak transcription	HSMMtube	muscle
28	chr17:59883400-59887400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr17:59883600-59887000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr17:59883600-59887000	Weak transcription	HSMM	muscle
31	chr17:59883600-59896800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr17:59883600-59898400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr17:59883800-59887000	Weak transcription	Fetal Lung	lung
34	chr17:59883800-59887000	Weak transcription	HMEC	breast
35	chr17:59883800-59887200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr17:59883800-59887200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr17:59883800-59887200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr17:59883800-59887200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr17:59883800-59887200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr17:59883800-59887200	Weak transcription	NH-A	brain
41	chr17:59883800-59893600	Weak transcription	GM12878-XiMat	blood
42	chr17:59883800-59898400	Weak transcription	A549	lung
43	chr17:59884000-59887200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr17:59884000-59887200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr17:59884000-59887200	Weak transcription	NHEK	skin
46	chr17:59884200-59887000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr17:59884200-59933200	Weak transcription	K562	blood
48	chr17:59884400-59887000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr17:59884400-59898000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr17:59884600-59887000	Weak transcription	Osteobl	bone

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