Variant report

Variant	rs1469543
Chromosome Location	chr2:9988327-9988328
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	chr2:9972444..9974015-chr2:9987549..9989213,2	MCF-7	breast:
5	chr2:9981404..9986079-chr2:9986481..9992681,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115750	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1014509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1036056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1036057	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1036058	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10495575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1062160	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs10929617	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10929618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1132838	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12468582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12470216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12476490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12478489	0.84[EUR][1000 genomes]
rs12611655	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12613533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12613568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12617615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12619769	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12621415	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12622420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12623017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12623213	0.83[EUR][1000 genomes]
rs12623372	0.80[ASN][1000 genomes]
rs1367386	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1469542	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1469544	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1469545	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]
rs1469546	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16867215	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs16867242	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1835427	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1967517	1.00[ASN][1000 genomes]
rs1967518	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280150	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2280151	0.91[ASN][1000 genomes]
rs2288644	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs4143791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143792	1.00[ASN][1000 genomes]
rs4143793	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs452480	0.95[CEU][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4610025	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4627538	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4668651	0.84[CHB][hapmap]
rs4669470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4669471	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4669472	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4669473	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4669475	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4669476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4669477	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4669478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4669479	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4669481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4669484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4669485	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4669486	0.91[ASN][1000 genomes]
rs4669488	0.91[ASN][1000 genomes]
rs59288259	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62127129	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62127130	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62127131	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62127132	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62127133	0.97[ASN][1000 genomes]
rs62127134	0.97[ASN][1000 genomes]
rs62127136	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62127137	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62127138	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62127140	0.94[ASN][1000 genomes]
rs62127143	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62127144	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62127145	0.92[ASN][1000 genomes]
rs62127146	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62127463	0.90[ASN][1000 genomes]
rs62127466	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62127471	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62127563	0.98[ASN][1000 genomes]
rs62127564	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62127565	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62129896	1.00[ASN][1000 genomes]
rs6707551	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs718255	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs718256	0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72782621	0.98[ASN][1000 genomes]
rs72782635	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7563385	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7579559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7602449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7608055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[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
rs1469543	TAF1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 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	chr2:9985200-9989600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:9985200-9995600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:9985200-9997200	Weak transcription	Fetal Heart	heart
20	chr2:9985400-9988400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:9985400-9989800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:9985400-9993800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:9985400-9995400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:9985400-9995400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:9985400-9995400	Weak transcription	Small Intestine	intestine
26	chr2:9985600-9989200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:9985600-9989600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr2:9985600-9989800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr2:9985600-9990600	Weak transcription	HSMMtube	muscle
30	chr2:9985600-9993800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:9985600-9995400	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:9985600-9997200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:9985800-9997000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:9986200-9988800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr2:9986200-9997800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:9986400-9993000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:9986600-9992200	Weak transcription	Fetal Intestine Small	intestine
38	chr2:9986600-9996200	Strong transcription	A549	lung
39	chr2:9986800-9990000	Weak transcription	Fetal Kidney	kidney
40	chr2:9986800-9990400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr2:9986800-9992400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr2:9987000-9989400	Weak transcription	GM12878-XiMat	blood
43	chr2:9987000-9990400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr2:9987000-9991200	Weak transcription	Gastric	stomach
45	chr2:9987200-9989400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:9987200-9990000	Weak transcription	Fetal Lung	lung
47	chr2:9987200-9990800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr2:9987200-10038400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr2:9987400-9988600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:9987400-9990000	Weak transcription	Fetal Intestine Large	intestine

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