Variant report

Variant	rs412039
Chromosome Location	chr2:10038890-10038891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10033449..10037613-chr2:10038043..10042119,5	MCF-7	breast:
2	chr2:10035308..10037799-chr2:10038582..10040182,2	MCF-7	breast:
3	chr2:10037000..10039031-chr2:10044234..10045895,2	MCF-7	breast:
4	chr2:10037949..10040040-chr2:10055239..10057291,2	MCF-7	breast:
5	chr2:9948070..9949733-chr2:10038866..10041132,2	K562	blood:
6	chr2:10037952..10040907-chr2:10047681..10050214,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs12466497	0.90[EUR][1000 genomes]
rs12477755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1709854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17364189	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2241664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287986	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs287999	0.83[AFR][1000 genomes]
rs34153848	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs35029226	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs369551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs369605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs375793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs382747	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs386355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388570	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs388695	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389002	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs391889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394650	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs395381	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs396281	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs400758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407874	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs408987	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs410121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414499	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs415676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs416228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs423651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs437662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs437906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs444650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447465	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs447476	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs448287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs450194	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs450286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs450643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs451045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs451412	0.83[AFR][1000 genomes]
rs452789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs453568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs453933	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669498	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4669499	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs499858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56010640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56102002	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56241824	0.90[EUR][1000 genomes]
rs56258032	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56382546	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432044	0.83[CEU][hapmap]
rs71437684	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv873631	chr2:9975557-10059770	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv873632	chr2:10000978-10045014	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	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
8	nsv1009210	chr2:10030072-10052257	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	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
10	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs412039	TAF1B	cis	Adipose Subcutaneous	GTEx
rs412039	RP11-95D17.1	cis	Adipose Subcutaneous	GTEx
rs412039	TAF1B	cis	Artery Tibial	GTEx
rs412039	TAF1B	cis	Esophagus Muscularis	GTEx
rs412039	TAF1B	cis	Skin Sun Exposed Lower leg	GTEx
rs412039	TAF1B	cis	Nerve Tibial	GTEx
rs412039	TAF1B	cis	lung	GTEx
rs412039	TAF1B	Cis_1M	lymphoblastoid	RTeQTL
rs412039	RP11-95D17.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9993800-10079600	Weak transcription	Gastric	stomach
2	chr2:9999200-10053800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:10014800-10045400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr2:10017800-10073000	Weak transcription	Right Ventricle	heart
5	chr2:10024400-10053800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr2:10024800-10047600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:10024800-10051400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:10025000-10047000	Weak transcription	Thymus	Thymus
9	chr2:10025000-10053800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:10025000-10053800	Weak transcription	Ovary	ovary
11	chr2:10025000-10054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:10025000-10054400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:10025000-10054400	Weak transcription	Spleen	Spleen
14	chr2:10025400-10052600	Weak transcription	Left Ventricle	heart
15	chr2:10026000-10072800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:10027000-10040400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:10027000-10047000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:10027400-10052200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:10027400-10053400	Weak transcription	Fetal Brain Male	brain
20	chr2:10027600-10052000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr2:10028200-10051000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:10028200-10053800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:10030400-10077200	Weak transcription	Aorta	Aorta
24	chr2:10030600-10080600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:10032600-10044600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:10032800-10044400	Weak transcription	Dnd41	blood
27	chr2:10033000-10044000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr2:10033000-10044400	Weak transcription	Primary B cells from cord blood	blood
29	chr2:10033000-10052800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:10033600-10041600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:10036000-10065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:10036200-10039000	Enhancers	NH-A	brain
33	chr2:10036400-10047800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:10036400-10052200	Weak transcription	Liver	Liver
35	chr2:10036600-10047600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:10036600-10076200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:10036800-10039400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:10036800-10039400	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr2:10036800-10051800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:10036800-10073000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:10037000-10039000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:10037000-10047400	Weak transcription	Fetal Intestine Large	intestine
43	chr2:10037200-10040400	Weak transcription	Placenta	Placenta
44	chr2:10037200-10044600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr2:10037200-10044600	Weak transcription	Fetal Thymus	thymus
46	chr2:10037200-10047200	Weak transcription	Primary T cells from cord blood	blood
47	chr2:10037200-10051800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:10037200-10080400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr2:10037600-10046000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:10037800-10040200	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links