Variant report

Variant	rs59288259
Chromosome Location	chr2:9987675-9987676
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9977777..9980395-chr2:9987504..9989873,2	MCF-7	breast:
2	chr2:9983867..9985746-chr2:9987128..9988771,2	K562	blood:
3	chr2:9981927..9985713-chr2:9987570..9993259,7	MCF-7	breast:
4	chr2:9985865..9987759-chr2:9990520..9994621,3	MCF-7	breast:
5	chr2:9985747..9988019-chr2:10062440..10064881,2	MCF-7	breast:
6	chr2:9986181..9988070-chr2:9991011..9993550,2	MCF-7	breast:
7	chr2:9972444..9974015-chr2:9987549..9989213,2	MCF-7	breast:
8	chr2:9981404..9986079-chr2:9986481..9992681,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115750	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1014509	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1036056	0.98[ASN][1000 genomes]
rs1036057	0.98[ASN][1000 genomes]
rs1036058	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10495575	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10929617	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10929618	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1132838	0.90[ASN][1000 genomes]
rs12468582	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12470216	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12476490	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12478489	0.82[EUR][1000 genomes]
rs12611655	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12613533	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12613568	0.97[ASN][1000 genomes]
rs12617615	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12619769	0.98[ASN][1000 genomes]
rs12621415	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12622420	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12623017	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12623213	0.81[EUR][1000 genomes]
rs12623372	0.80[ASN][1000 genomes]
rs1367386	0.91[ASN][1000 genomes]
rs1469542	1.00[ASN][1000 genomes]
rs1469543	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469544	1.00[ASN][1000 genomes]
rs1469545	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469546	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473962	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867195	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867196	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867211	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16867215	0.92[ASN][1000 genomes]
rs16867242	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1835427	0.90[ASN][1000 genomes]
rs1967517	1.00[ASN][1000 genomes]
rs1967518	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280150	0.91[ASN][1000 genomes]
rs2280151	0.91[ASN][1000 genomes]
rs4143791	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143792	1.00[ASN][1000 genomes]
rs4143793	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs452480	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4610025	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4627538	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4669470	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4669471	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4669472	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4669473	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4669475	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4669476	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4669477	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4669478	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4669479	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4669481	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4669484	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4669485	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4669486	0.91[ASN][1000 genomes]
rs4669488	0.91[ASN][1000 genomes]
rs62127129	0.86[EUR][1000 genomes]
rs62127130	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62127131	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62127132	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62127133	0.97[ASN][1000 genomes]
rs62127134	0.97[ASN][1000 genomes]
rs62127136	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62127137	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62127138	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62127140	0.94[ASN][1000 genomes]
rs62127143	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62127144	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62127145	0.92[ASN][1000 genomes]
rs62127146	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62127463	0.90[ASN][1000 genomes]
rs62127466	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62127471	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62127563	0.98[ASN][1000 genomes]
rs62127564	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62127565	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62129896	1.00[ASN][1000 genomes]
rs6707551	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs718255	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs718256	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72782621	0.98[ASN][1000 genomes]
rs72782635	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7563385	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7579559	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7602449	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7608055	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59288259	TAF1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9984200-9994000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:9984600-9990600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:9984600-9992600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:9984600-9995400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:9984800-9997600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:9984800-9998400	Weak transcription	Pancreas	Pancrea
7	chr2:9985000-9990400	Weak transcription	Brain Angular Gyrus	brain
8	chr2:9985000-9990800	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:9985000-9991000	Weak transcription	Colonic Mucosa	Colon
10	chr2:9985000-9992000	Weak transcription	Brain Substantia Nigra	brain
11	chr2:9985000-9992000	Weak transcription	Lung	lung
12	chr2:9985000-9992000	Weak transcription	Ovary	ovary
13	chr2:9985000-9992200	Weak transcription	Fetal Stomach	stomach
14	chr2:9985000-9992200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:9985000-9993600	Weak transcription	Right Ventricle	heart
16	chr2:9985000-10000800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr2:9985200-9987800	Genic enhancers	Dnd41	blood
18	chr2:9985200-9987800	Enhancers	Hela-S3	cervix
19	chr2:9985200-9987800	Enhancers	HMEC	breast
20	chr2:9985200-9987800	Genic enhancers	Osteobl	bone
21	chr2:9985200-9989600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:9985200-9995600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:9985200-9997200	Weak transcription	Fetal Heart	heart
24	chr2:9985400-9988200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:9985400-9988400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:9985400-9989800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:9985400-9993800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr2:9985400-9995400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:9985400-9995400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:9985400-9995400	Weak transcription	Small Intestine	intestine
31	chr2:9985600-9987800	Strong transcription	Adipose Nuclei	Adipose
32	chr2:9985600-9987800	Strong transcription	Brain Anterior Caudate	brain
33	chr2:9985600-9987800	Strong transcription	HSMM	muscle
34	chr2:9985600-9988200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:9985600-9988200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:9985600-9989200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:9985600-9989600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr2:9985600-9989800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr2:9985600-9990600	Weak transcription	HSMMtube	muscle
40	chr2:9985600-9993800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:9985600-9995400	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr2:9985600-9997200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:9985800-9987800	Genic enhancers	Primary T cells fromperipheralblood	blood
44	chr2:9985800-9997000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:9986000-9987800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:9986000-9987800	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr2:9986000-9987800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:9986000-9987800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
49	chr2:9986000-9987800	Strong transcription	Fetal Muscle Trunk	muscle
50	chr2:9986000-9987800	Strong transcription	Fetal Muscle Leg	muscle

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