Variant report

Variant	rs62127563
Chromosome Location	chr2:9998529-9998530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:9982413..9984007-chr2:9997809..10000027,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115750	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1014509	1.00[ASN][1000 genomes]
rs1036056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036058	0.93[ASN][1000 genomes]
rs10495575	0.98[ASN][1000 genomes]
rs1062160	0.81[ASN][1000 genomes]
rs10929617	0.97[ASN][1000 genomes]
rs10929618	0.95[ASN][1000 genomes]
rs1132838	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12468582	0.95[ASN][1000 genomes]
rs12470216	0.98[ASN][1000 genomes]
rs12476490	0.95[ASN][1000 genomes]
rs12478489	0.81[ASN][1000 genomes]
rs12611655	0.97[ASN][1000 genomes]
rs12613533	0.98[ASN][1000 genomes]
rs12613568	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12617615	0.98[ASN][1000 genomes]
rs12619769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621415	0.99[ASN][1000 genomes]
rs12622420	0.98[ASN][1000 genomes]
rs12623017	0.98[ASN][1000 genomes]
rs12623372	0.82[ASN][1000 genomes]
rs1367386	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1469542	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1469543	0.98[ASN][1000 genomes]
rs1469544	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1469545	0.98[ASN][1000 genomes]
rs1469546	0.98[ASN][1000 genomes]
rs1473962	0.98[ASN][1000 genomes]
rs16867195	0.98[ASN][1000 genomes]
rs16867196	0.98[ASN][1000 genomes]
rs16867211	0.97[ASN][1000 genomes]
rs16867215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16867242	0.91[ASN][1000 genomes]
rs1835427	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1967517	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1967518	0.98[ASN][1000 genomes]
rs2280150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4143791	0.98[ASN][1000 genomes]
rs4143792	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4143793	0.97[ASN][1000 genomes]
rs452480	0.88[ASN][1000 genomes]
rs4610025	0.98[ASN][1000 genomes]
rs4627538	0.95[ASN][1000 genomes]
rs4669470	0.99[ASN][1000 genomes]
rs4669471	1.00[ASN][1000 genomes]
rs4669472	1.00[ASN][1000 genomes]
rs4669473	1.00[ASN][1000 genomes]
rs4669475	0.98[ASN][1000 genomes]
rs4669476	0.97[ASN][1000 genomes]
rs4669477	0.97[ASN][1000 genomes]
rs4669478	0.97[ASN][1000 genomes]
rs4669479	0.95[ASN][1000 genomes]
rs4669481	0.95[ASN][1000 genomes]
rs4669484	0.94[ASN][1000 genomes]
rs4669485	0.92[ASN][1000 genomes]
rs4669486	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4669488	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4669501	0.81[ASN][1000 genomes]
rs59288259	0.98[ASN][1000 genomes]
rs62127130	0.98[ASN][1000 genomes]
rs62127131	0.83[ASN][1000 genomes]
rs62127133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62127134	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62127136	0.98[ASN][1000 genomes]
rs62127137	0.94[ASN][1000 genomes]
rs62127138	0.97[ASN][1000 genomes]
rs62127140	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62127143	0.95[ASN][1000 genomes]
rs62127144	0.95[ASN][1000 genomes]
rs62127145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62127146	0.94[ASN][1000 genomes]
rs62127463	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62127466	0.90[ASN][1000 genomes]
rs62127471	0.82[ASN][1000 genomes]
rs62127564	1.00[ASN][1000 genomes]
rs62127565	1.00[ASN][1000 genomes]
rs62129896	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6707551	1.00[ASN][1000 genomes]
rs718255	0.92[ASN][1000 genomes]
rs718256	0.92[ASN][1000 genomes]
rs72782621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72782635	0.97[ASN][1000 genomes]
rs7563385	0.98[ASN][1000 genomes]
rs7579559	1.00[ASN][1000 genomes]
rs7602449	0.95[ASN][1000 genomes]
rs7608055	1.00[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	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
8	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
9	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62127563	TAF1B	cis	Nerve Tibial	GTEx
rs62127563	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	chr2:9985000-10000800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:9987200-10038400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:9987400-10003200	Weak transcription	Stomach Mucosa	stomach
4	chr2:9989400-9999200	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:9989400-10000600	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr2:9989400-10001000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr2:9989600-9999200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
8	chr2:9989600-9999400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:9989600-10001200	Strong transcription	Osteobl	bone
10	chr2:9989800-9999200	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:9990000-9998600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:9990200-9998800	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr2:9990400-10000600	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr2:9990400-10000800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:9990600-9998600	Strong transcription	Brain Anterior Caudate	brain
16	chr2:9990600-9999200	Strong transcription	Left Ventricle	heart
17	chr2:9990600-10000800	Strong transcription	Stomach Smooth Muscle	stomach
18	chr2:9990600-10001600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:9990800-9999000	Strong transcription	Brain Hippocampus Middle	brain
20	chr2:9991000-9998800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:9992000-9998600	Strong transcription	Ovary	ovary
22	chr2:9992000-9999000	Strong transcription	Brain Cingulate Gyrus	brain
23	chr2:9993000-10003600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:9993200-10001200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:9993600-10007400	Weak transcription	Psoas Muscle	Psoas
26	chr2:9993800-10002600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
27	chr2:9993800-10002800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:9993800-10079600	Weak transcription	Gastric	stomach
29	chr2:9994600-10000600	Weak transcription	Right Ventricle	heart
30	chr2:9995400-9999000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
31	chr2:9995400-10001200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
32	chr2:9995400-10002600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:9995400-10002800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:9995600-10002600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
35	chr2:9995800-10001200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
36	chr2:9995800-10001400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
37	chr2:9995800-10038000	Weak transcription	Small Intestine	intestine
38	chr2:9996000-10001200	ZNF genes & repeats	Fetal Brain Female	brain
39	chr2:9996000-10001200	ZNF genes & repeats	Dnd41	blood
40	chr2:9996000-10001600	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:9996200-10001000	ZNF genes & repeats	A549	lung
42	chr2:9996400-9998600	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:9996400-10001600	ZNF genes & repeats	Brain Germinal Matrix	brain
44	chr2:9996400-10016000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:9996600-10001400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:9996800-9999200	ZNF genes & repeats	GM12878-XiMat	blood
47	chr2:9996800-10001400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:9996800-10001400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:9997000-9999000	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:9997000-9999200	ZNF genes & repeats	HepG2	liver

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