Variant report

Variant	rs17389198
Chromosome Location	chr1:209922058-209922059
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209917192..209919277-chr1:209920875..209922464,2	K562	blood:
2	chr1:209921622..209924785-chr1:209954989..209957828,3	MCF-7	breast:
3	chr1:209920122..209922907-chr1:209973621..209976183,2	MCF-7	breast:
4	chr1:209921608..209924525-chr1:209928498..209931459,3	K562	blood:
5	chr1:209921083..209924525-chr1:209927225..209931869,7	K562	blood:
6	chr1:209916474..209918920-chr1:209920104..209922211,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000009790	Chromatin interaction
ENSG00000117595	Chromatin interaction
ENSG00000236136	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1000282	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1000283	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1007693	0.86[CEU][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10157973	1.00[CEU][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10489342	0.83[ASN][1000 genomes]
rs10863783	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10863785	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11119327	0.95[CEU][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11119328	0.80[AMR][1000 genomes]
rs11119330	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11119331	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11119332	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11119336	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119338	1.00[JPT][hapmap]
rs11119340	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11119341	0.80[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11485195	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11487866	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11487867	0.86[CEU][hapmap];0.82[AMR][1000 genomes]
rs11806703	0.86[AMR][1000 genomes]
rs11807619	0.81[YRI][hapmap];0.88[AMR][1000 genomes]
rs11808690	0.80[CEU][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11811440	0.86[AMR][1000 genomes]
rs12030655	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12034758	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12059226	0.95[CEU][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12060420	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12060922	0.95[CEU][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12086634	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12090931	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12094117	0.95[CEU][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12116437	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12120361	0.95[CEU][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12129718	0.80[EUR][1000 genomes]
rs12131636	0.81[ASN][1000 genomes]
rs12138452	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1415542	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1415544	0.80[EUR][1000 genomes]
rs1474654	0.88[AMR][1000 genomes]
rs1474655	0.88[AMR][1000 genomes]
rs17389184	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1999826	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2076150	0.83[ASN][1000 genomes]
rs2236903	0.90[CEU][hapmap]
rs2272867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2282738	0.85[CEU][hapmap]
rs2282739	0.90[CEU][hapmap]
rs3765240	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3766618	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs3766619	0.95[CEU][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3817821	0.85[EUR][1000 genomes]
rs4844891	0.90[CEU][hapmap]
rs61820570	0.88[AMR][1000 genomes]
rs627670	1.00[CEU][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs643118	0.83[ASN][1000 genomes]
rs6540549	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6540550	1.00[CEU][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6540551	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6540552	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6540553	1.00[CEU][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6540554	0.85[CEU][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs6540555	0.87[ASN][1000 genomes]
rs6540556	0.88[ASN][1000 genomes]
rs6665715	1.00[CEU][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6672256	0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs667681	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6679099	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6679405	1.00[CEU][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6685077	0.81[CEU][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs6691905	0.81[ASN][1000 genomes]
rs6696463	0.83[ASN][1000 genomes]
rs6702301	1.00[CEU][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6752	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs679846	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7521461	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7532324	0.87[EUR][1000 genomes]
rs7536882	0.90[ASN][1000 genomes]
rs7539852	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7548219	0.91[ASN][1000 genomes]
rs7548781	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs909710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs932335	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9430012	0.95[CEU][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9430014	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9430016	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs9430017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1001588	chr1:209908876-209938243	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17389198	TRAF3IP3	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209919600-209922400	Enhancers	Fetal Heart	heart
2	chr1:209919800-209923400	Enhancers	Fetal Intestine Small	intestine
3	chr1:209920800-209922200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:209920800-209922200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:209920800-209922200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:209920800-209922200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr1:209920800-209922400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr1:209921400-209922200	Enhancers	Fetal Intestine Large	intestine
9	chr1:209921400-209922400	Enhancers	Fetal Thymus	thymus
10	chr1:209921400-209922600	Enhancers	Primary B cells from cord blood	blood
11	chr1:209921400-209922600	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr1:209921400-209923400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:209921400-209923400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:209921400-209925200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:209921400-209929800	Weak transcription	Right Atrium	heart
16	chr1:209921400-209930000	Weak transcription	Right Ventricle	heart
17	chr1:209921600-209922200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
18	chr1:209921600-209922200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
19	chr1:209921600-209922200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
20	chr1:209921600-209922200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:209921600-209922200	Enhancers	Primary B cells from peripheral blood	blood
22	chr1:209921600-209922200	Enhancers	Primary hematopoietic stem cells	blood
23	chr1:209921600-209922200	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr1:209921600-209922400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
25	chr1:209921600-209922400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:209921600-209922800	Enhancers	GM12878-XiMat	blood
27	chr1:209921600-209923200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:209921600-209924800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr1:209921600-209926600	Enhancers	Primary T cells fromperipheralblood	blood
30	chr1:209921600-209926600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:209921600-209926800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr1:209921800-209922200	Weak transcription	Thymus	Thymus
33	chr1:209921800-209922400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:209921800-209922400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:209921800-209922800	Weak transcription	Liver	Liver
36	chr1:209921800-209924200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:209921800-209924200	Weak transcription	A549	lung
38	chr1:209921800-209924600	Enhancers	Primary T cells from cord blood	blood
39	chr1:209921800-209924600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr1:209921800-209924800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:209921800-209924800	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr1:209921800-209924800	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr1:209921800-209925000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:209921800-209925400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:209921800-209925400	Weak transcription	K562	blood
46	chr1:209921800-209929600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:209921800-209930000	Weak transcription	Stomach Mucosa	stomach
48	chr1:209921800-209940800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:209921800-209942000	Weak transcription	Pancreas	Pancrea
50	chr1:209922000-209922400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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