Variant report

Variant	rs17364189
Chromosome Location	chr2:10064791-10064792
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9985747..9988019-chr2:10062440..10064881,2	MCF-7	breast:
2	chr2:10054070..10056636-chr2:10061535..10064977,4	MCF-7	breast:
3	chr2:10053405..10055914-chr2:10061703..10065567,3	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs12466497	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12477755	0.96[CEU][hapmap];0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1709854	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2241664	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs287986	0.85[YRI][hapmap]
rs34153848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35029226	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs369551	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs369605	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs371305	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs372031	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs374197	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs375793	0.96[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs382747	1.00[YRI][hapmap]
rs386355	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs388570	0.80[MKK][hapmap];1.00[YRI][hapmap]
rs388695	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs389002	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs391889	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs394650	0.81[AFR][1000 genomes]
rs395381	0.90[EUR][1000 genomes]
rs396281	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs397498	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs397871	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs400758	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs403317	0.96[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs407874	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs408987	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs410121	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs411413	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs412039	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs414499	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs415676	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs416228	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs417271	0.94[LWK][hapmap]
rs420122	0.96[CEU][hapmap];0.88[JPT][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs421030	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs423651	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs431519	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs431562	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs437662	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs437906	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs438762	0.96[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs438966	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs439310	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs444650	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs447465	0.84[MKK][hapmap];1.00[YRI][hapmap]
rs447476	0.92[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs448287	0.96[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs449472	0.96[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs450194	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs450286	0.96[CEU][hapmap];0.80[CHD][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs450643	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs451045	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs452789	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs453568	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs453933	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs454269	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4669496	0.83[AFR][1000 genomes]
rs4669498	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669499	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499858	0.96[CEU][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs56010640	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs56102002	0.86[AFR][1000 genomes]
rs56241824	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56258032	0.84[EUR][1000 genomes]
rs56382546	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6432044	0.82[CEU][hapmap]
rs71437684	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][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	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv580960	chr2:9993451-10066694	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv1006533	chr2:10030964-10065624	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1004743	chr2:10031389-10065624	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1005938	chr2:10043181-10074384	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs17364189	TAF1B	Cis_1M	lymphoblastoid	RTeQTL
rs17364189	TAF1B	cis	Muscle Skeletal	GTEx
rs17364189	TAF1B	cis	Skin Sun Exposed Lower leg	GTEx
rs17364189	TAF1B	cis	cerebellum	SCAN
rs17364189	RP11-95D17.1	cis	Adipose Subcutaneous	GTEx
rs17364189	TAF1B	cis	Artery Tibial	GTEx
rs17364189	TAF1B	cis	Adipose Subcutaneous	GTEx
rs17364189	TAF1B	cis	Nerve Tibial	GTEx
rs17364189	TAF1B	cis	Esophagus Muscularis	GTEx
rs17364189	TAF1B	cis	lung	GTEx
rs17364189	TAF1B	cis	multi-tissue	Pritchard
rs17364189	RP11-95D17.1	cis	Skin Sun Exposed Lower leg	GTEx
rs17364189	TAF1B	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9993800-10079600	Weak transcription	Gastric	stomach
2	chr2:10017800-10073000	Weak transcription	Right Ventricle	heart
3	chr2:10026000-10072800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:10030400-10077200	Weak transcription	Aorta	Aorta
5	chr2:10030600-10080600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:10036000-10065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:10036600-10076200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:10036800-10073000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:10037200-10080400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:10037800-10075600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:10038600-10079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:10038600-10081400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:10042600-10077000	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:10044200-10065200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:10045800-10079600	Weak transcription	Esophagus	oesophagus
16	chr2:10046000-10075200	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:10047200-10080000	Weak transcription	Colonic Mucosa	Colon
18	chr2:10049000-10077400	Weak transcription	Brain Anterior Caudate	brain
19	chr2:10049400-10077200	Weak transcription	Brain Angular Gyrus	brain
20	chr2:10049400-10081000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:10049600-10065200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr2:10049600-10081200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:10052800-10076600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:10053200-10077800	Weak transcription	Liver	Liver
25	chr2:10054600-10073400	Weak transcription	Brain Substantia Nigra	brain
26	chr2:10054800-10065000	Weak transcription	Lung	lung
27	chr2:10054800-10066000	Weak transcription	Fetal Brain Male	brain
28	chr2:10054800-10069200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:10054800-10072200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:10054800-10079000	Weak transcription	Fetal Kidney	kidney
31	chr2:10055000-10064800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:10055000-10067600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:10055000-10072600	Weak transcription	Spleen	Spleen
34	chr2:10055000-10080800	Weak transcription	Pancreas	Pancrea
35	chr2:10055000-10080800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr2:10055000-10081800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:10055200-10072600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:10055200-10072800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:10055200-10073200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:10055200-10079600	Weak transcription	K562	blood
41	chr2:10055200-10080800	Weak transcription	HMEC	breast
42	chr2:10055600-10073000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:10055800-10075800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:10056800-10074200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:10057400-10065000	Strong transcription	Dnd41	blood
46	chr2:10058000-10065200	Strong transcription	Fetal Thymus	thymus
47	chr2:10058800-10076000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:10059000-10080600	Weak transcription	HSMMtube	muscle
49	chr2:10059200-10068000	Weak transcription	Psoas Muscle	Psoas
50	chr2:10059200-10072800	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links