Variant report

Variant	rs62127138
Chromosome Location	chr2:10015245-10015246
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10013311..10015489-chr2:10017066..10019345,2	MCF-7	breast:

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1014509	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1036056	0.97[ASN][1000 genomes]
rs1036057	0.97[ASN][1000 genomes]
rs1036058	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10495575	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1062160	0.84[ASN][1000 genomes]
rs10929617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929618	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1132838	0.95[ASN][1000 genomes]
rs12468582	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12470216	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12476490	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12478489	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12611655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12613533	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12613568	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12617615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12619769	0.97[ASN][1000 genomes]
rs12621415	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12622420	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12623017	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12623213	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12623372	0.85[ASN][1000 genomes]
rs1367386	0.95[ASN][1000 genomes]
rs1469542	0.95[ASN][1000 genomes]
rs1469543	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1469544	0.95[ASN][1000 genomes]
rs1469545	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1469546	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1473962	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16867195	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16867196	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16867211	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867215	0.97[ASN][1000 genomes]
rs16867242	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1835427	0.95[ASN][1000 genomes]
rs1967517	0.95[ASN][1000 genomes]
rs1967518	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2280150	0.95[ASN][1000 genomes]
rs2280151	0.95[ASN][1000 genomes]
rs2288640	0.81[ASN][1000 genomes]
rs2288644	0.82[ASN][1000 genomes]
rs4143791	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4143792	0.95[ASN][1000 genomes]
rs4143793	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs452480	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4610025	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4627538	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4669470	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4669471	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4669472	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4669473	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4669475	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4669476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669477	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669479	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4669481	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4669484	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4669485	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4669486	0.95[ASN][1000 genomes]
rs4669488	0.95[ASN][1000 genomes]
rs4669501	0.84[ASN][1000 genomes]
rs4669506	0.82[ASN][1000 genomes]
rs59288259	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62127129	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62127130	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62127131	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62127132	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62127133	0.98[ASN][1000 genomes]
rs62127134	0.98[ASN][1000 genomes]
rs62127136	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62127137	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62127140	0.98[ASN][1000 genomes]
rs62127143	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62127144	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62127145	0.97[ASN][1000 genomes]
rs62127146	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62127463	0.95[ASN][1000 genomes]
rs62127466	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62127471	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62127563	0.97[ASN][1000 genomes]
rs62127564	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62127565	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62129896	0.95[ASN][1000 genomes]
rs6707551	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6743707	0.87[AFR][1000 genomes]
rs6743866	0.87[AFR][1000 genomes]
rs6753379	0.87[AFR][1000 genomes]
rs718255	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs718256	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72782621	0.97[ASN][1000 genomes]
rs72782635	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559653	0.83[AFR][1000 genomes]
rs7563385	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7579559	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7602449	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7608055	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62127138	TAF1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9987200-10038400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:9993800-10079600	Weak transcription	Gastric	stomach
3	chr2:9995800-10038000	Weak transcription	Small Intestine	intestine
4	chr2:9996400-10016000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:9998200-10024000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:9998200-10035600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:9998600-10017000	Weak transcription	K562	blood
8	chr2:9998600-10024000	Weak transcription	Pancreas	Pancrea
9	chr2:9998800-10026000	Weak transcription	Fetal Brain Male	brain
10	chr2:9998800-10032200	Weak transcription	Fetal Heart	heart
11	chr2:9998800-10036400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:9999000-10015400	Weak transcription	HUVEC	blood vessel
13	chr2:9999000-10017600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:9999000-10024000	Weak transcription	Colonic Mucosa	Colon
15	chr2:9999000-10024000	Weak transcription	Spleen	Spleen
16	chr2:9999000-10035800	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:9999000-10035800	Weak transcription	Brain Substantia Nigra	brain
18	chr2:9999000-10037000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:9999000-10037200	Weak transcription	Colon Smooth Muscle	Colon
20	chr2:9999200-10017000	Weak transcription	HSMMtube	muscle
21	chr2:9999200-10017600	Weak transcription	Brain Anterior Caudate	brain
22	chr2:9999200-10036200	Weak transcription	Brain Angular Gyrus	brain
23	chr2:9999200-10036400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:9999200-10053800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:10001000-10018400	Weak transcription	NHLF	lung
26	chr2:10001600-10024000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:10001600-10024000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:10002200-10024200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:10002600-10016800	Weak transcription	HMEC	breast
30	chr2:10002600-10017000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr2:10007400-10020000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:10007400-10020400	Strong transcription	Primary T cells from cord blood	blood
33	chr2:10007800-10016800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:10007800-10017000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:10007800-10021000	Strong transcription	A549	lung
36	chr2:10007800-10026200	Strong transcription	Dnd41	blood
37	chr2:10008000-10017000	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:10008000-10017000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:10008000-10026800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:10008200-10019600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:10008200-10020200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:10008200-10028000	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr2:10008400-10026600	Weak transcription	GM12878-XiMat	blood
44	chr2:10008600-10020800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:10008600-10021000	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr2:10008800-10018400	Weak transcription	Psoas Muscle	Psoas
47	chr2:10008800-10021000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:10009000-10016800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:10009000-10024000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr2:10009200-10016200	Strong transcription	Fetal Stomach	stomach

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