Variant report

Variant	rs287987
Chromosome Location	chr2:9986162-9986163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9983066..9987186-chr2:10091615..10095343,4	MCF-7	breast:
2	chr2:9984016..9986818-chr2:10112280..10114129,2	MCF-7	breast:
3	chr2:9985865..9987759-chr2:9990520..9994621,3	MCF-7	breast:
4	chr2:9985747..9988019-chr2:10062440..10064881,2	MCF-7	breast:
5	chr2:9984123..9986772-chr2:10086772..10088957,2	K562	blood:
6	chr2:9982271..9986804-chr2:10090021..10093067,7	K562	blood:

Variant related genes	Relation type
ENSG00000134317	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11692193	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13008782	0.84[ASN][1000 genomes]
rs287972	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs287974	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs287986	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287988	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs287992	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs287993	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287994	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287995	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287996	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287997	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs287999	1.00[ASN][1000 genomes]
rs382747	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs388570	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs447465	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs451412	0.93[ASN][1000 genomes]
rs514805	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs572907	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731044	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599798	0.82[EUR][1000 genomes];1.00[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	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	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
4	nsv873629	chr2:9949464-10016627	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
5	nsv873630	chr2:9953949-10030024	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
6	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
7	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs287987	TAF1B	cis	lung	GTEx
rs287987	TAF1B	cis	Esophagus Muscularis	GTEx
rs287987	TAF1B	cis	Nerve Tibial	GTEx
rs287987	TAF1B	Cis_1M	lymphoblastoid	RTeQTL
rs287987	TAF1B	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9984200-9986200	Weak transcription	Spleen	Spleen
2	chr2:9984200-9994000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:9984400-9986200	Weak transcription	Aorta	Aorta
4	chr2:9984400-9986400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:9984400-9987400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:9984600-9986200	Weak transcription	Fetal Intestine Large	intestine
7	chr2:9984600-9986200	Weak transcription	Left Ventricle	heart
8	chr2:9984600-9986400	Weak transcription	Gastric	stomach
9	chr2:9984600-9990600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:9984600-9992600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:9984600-9995400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:9984800-9997600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr2:9984800-9998400	Weak transcription	Pancreas	Pancrea
14	chr2:9985000-9986200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:9985000-9986200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:9985000-9986200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:9985000-9986200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:9985000-9986200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:9985000-9986200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:9985000-9986200	Weak transcription	Liver	Liver
21	chr2:9985000-9986200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:9985000-9986200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:9985000-9986200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:9985000-9986200	Enhancers	Placenta	Placenta
25	chr2:9985000-9986200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:9985000-9986200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:9985000-9986200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:9985000-9986200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:9985000-9986200	Enhancers	HepG2	liver
30	chr2:9985000-9987200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:9985000-9987200	Weak transcription	Psoas Muscle	Psoas
32	chr2:9985000-9990400	Weak transcription	Brain Angular Gyrus	brain
33	chr2:9985000-9990800	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:9985000-9991000	Weak transcription	Colonic Mucosa	Colon
35	chr2:9985000-9992000	Weak transcription	Brain Substantia Nigra	brain
36	chr2:9985000-9992000	Weak transcription	Lung	lung
37	chr2:9985000-9992000	Weak transcription	Ovary	ovary
38	chr2:9985000-9992200	Weak transcription	Fetal Stomach	stomach
39	chr2:9985000-9992200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:9985000-9993600	Weak transcription	Right Ventricle	heart
41	chr2:9985000-10000800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr2:9985200-9986200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr2:9985200-9986200	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:9985200-9986200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr2:9985200-9986200	Enhancers	HUVEC	blood vessel
46	chr2:9985200-9986600	Genic enhancers	Fetal Lung	lung
47	chr2:9985200-9987200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr2:9985200-9987800	Genic enhancers	Dnd41	blood
49	chr2:9985200-9987800	Enhancers	Hela-S3	cervix
50	chr2:9985200-9987800	Enhancers	HMEC	breast

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