Variant report

Variant	rs1980429
Chromosome Location	chr11:9010474-9010475
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr11:9009860-9010501	K562	blood:	n/a	chr11:9010331-9010341 chr11:9010333-9010350 chr11:9010332-9010339 chr11:9010332-9010341 chr11:9010384-9010393 chr11:9010325-9010346 chr11:9010332-9010339 chr11:9010332-9010339
2	GATA3	chr11:9010137-9010706	SK-N-SH	brain:	n/a	chr11:9010331-9010341 chr11:9010333-9010350 chr11:9010533-9010546 chr11:9010332-9010339 chr11:9010332-9010341 chr11:9010384-9010393 chr11:9010325-9010346 chr11:9010332-9010339 chr11:9010535-9010543 chr11:9010332-9010339
3	JUN	chr11:9009950-9010572	K562	blood:	n/a	chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010386-9010394 chr11:9010385-9010395
4	TBL1XR1	chr11:9010022-9010501	K562	blood:	n/a	n/a
5	GABPA	chr11:9009871-9010522	K562	blood:	n/a	n/a
6	MAX	chr11:9010216-9010598	K562	blood:	n/a	n/a
7	POLR2A	chr11:9009834-9010605	K562	blood:	n/a	n/a
8	MAFK	chr11:9010025-9010653	K562	blood:	n/a	n/a
9	HMGN3	chr11:9009856-9010491	K562	blood:	n/a	chr11:9010387-9010396
10	FOS	chr11:9010190-9010557	K562	blood:	n/a	chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010386-9010394 chr11:9010385-9010395
11	MYC	chr11:9009854-9010526	K562	blood:	n/a	n/a
12	POLR2A	chr11:9010119-9010568	K562	blood:	n/a	n/a
13	GATA2	chr11:9009787-9010646	K562	blood:	n/a	chr11:9010331-9010341 chr11:9010333-9010350 chr11:9010533-9010546 chr11:9010332-9010339 chr11:9010332-9010341 chr11:9010384-9010393 chr11:9010325-9010346 chr11:9009840-9009851 chr11:9010332-9010339 chr11:9010535-9010543 chr11:9010332-9010339
14	SMARCB1	chr11:9009830-9010745	K562	blood:	n/a	chr11:9010386-9010395
15	TBP	chr11:9010267-9010509	K562	blood:	n/a	n/a
16	BHLHE40	chr11:9009989-9010608	K562	blood:	n/a	n/a
17	MAX	chr11:9010043-9010612	K562	blood:	n/a	n/a
18	RCOR1	chr11:9009812-9010638	K562	blood:	n/a	n/a
19	IRF1	chr11:9009884-9010619	K562	blood:	n/a	n/a
20	GATA2	chr11:9009859-9010566	K562	blood:	n/a	chr11:9010331-9010341 chr11:9010333-9010350 chr11:9010533-9010546 chr11:9010332-9010339 chr11:9010332-9010341 chr11:9010384-9010393 chr11:9010325-9010346 chr11:9010332-9010339 chr11:9010535-9010543 chr11:9010332-9010339
21	GATA3	chr11:9010112-9010644	SK-N-SH	brain:	n/a	chr11:9010331-9010341 chr11:9010333-9010350 chr11:9010533-9010546 chr11:9010332-9010339 chr11:9010332-9010341 chr11:9010384-9010393 chr11:9010325-9010346 chr11:9010332-9010339 chr11:9010535-9010543 chr11:9010332-9010339
22	STAT5A	chr11:9009786-9010635	K562	blood:	n/a	n/a
23	EP300	chr11:9009861-9010612	K562	blood:	n/a	n/a
24	TBL1XR1	chr11:9009946-9010610	K562	blood:	n/a	n/a
25	TEAD4	chr11:9009771-9011748	K562	blood:	n/a	n/a
26	PML	chr11:9009843-9010607	K562	blood:	n/a	n/a
27	PML	chr11:9009771-9010635	K562	blood:	n/a	n/a
28	CEBPB	chr11:9009845-9010496	K562	blood:	n/a	n/a
29	MAZ	chr11:9009992-9010557	K562	blood:	n/a	n/a
30	HDAC2	chr11:9009829-9010595	K562	blood:	n/a	chr11:9010141-9010155
31	ATF3	chr11:9010135-9010595	K562	blood:	n/a	n/a
32	CCNT2	chr11:9009733-9010551	K562	blood:	n/a	chr11:9010330-9010350
33	HDAC2	chr11:9010157-9010580	K562	blood:	n/a	n/a
34	TEAD4	chr11:9009765-9010691	K562	blood:	n/a	n/a
35	E2F6	chr11:9010310-9010531	K562	blood:	n/a	n/a
36	POLR2A	chr11:9009750-9010654	K562	blood:	n/a	n/a
37	NR2F2	chr11:9009827-9010569	K562	blood:	n/a	n/a
38	TRIM28	chr11:9009773-9010679	K562	blood:	n/a	n/a
39	ZNF143	chr11:9010034-9010502	K562	blood:	n/a	n/a
40	FOSL1	chr11:9010209-9010508	K562	blood:	n/a	chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010386-9010394 chr11:9010385-9010395 chr11:9010384-9010395
41	REST	chr11:9010210-9010496	K562	blood:	n/a	n/a
42	MAFK	chr11:9010293-9010588	IMR90	lung:	n/a	n/a
43	STAT5A	chr11:9009803-9010599	K562	blood:	n/a	n/a
44	CBX3	chr11:9009915-9010632	K562	blood:	n/a	n/a
45	ZNF274	chr11:9010037-9010506	K562	blood:	n/a	n/a
46	POLR2A	chr11:9009863-9010539	K562	blood:	n/a	n/a
47	MAFF	chr11:9009908-9010598	K562	blood:	n/a	n/a
48	JUN	chr11:9010020-9010633	K562	blood:	n/a	chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010386-9010394 chr11:9010385-9010395
49	EP300	chr11:9009931-9010512	K562	blood:	n/a	n/a
50	JUN	chr11:9009512-9011924	K562	blood:	n/a	chr11:9010385-9010395 chr11:9011084-9011092 chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010386-9010394 chr11:9011083-9011093 chr11:9010385-9010395 chr11:9011200-9011209 chr11:9011085-9011096 chr11:9011084-9011091

No.	Distal block	Cell Line	Cell type
1	chr11:8992487..8994704-chr11:9009691..9012434,3	K562	blood:
2	chr11:8981281..8983336-chr11:9009757..9012558,2	K562	blood:
3	chr11:9008310..9013368-chr11:9022083..9026889,11	K562	blood:
4	chr11:9010207..9011708-chr11:9012903..9015577,2	K562	blood:

Variant related genes	Relation type
NRIP3	TF binding region
ENSG00000253973	Chromatin interaction
ENSG00000175352	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10743093	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10769967	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs10769970	0.85[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10769971	0.87[JPT][hapmap]
rs10769973	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10769979	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769980	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769981	0.84[ASN][1000 genomes]
rs10840130	0.82[JPT][hapmap]
rs10840134	0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10840141	0.85[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10840142	0.85[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10840147	0.88[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap]
rs10840148	0.84[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap]
rs10840157	0.98[ASN][1000 genomes]
rs10840158	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042078	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs11042103	0.85[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap]
rs11042125	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs11042149	0.96[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042150	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11042151	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11042152	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042154	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1109305	0.83[ASN][1000 genomes]
rs1123936	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11603841	0.88[CEU][hapmap]
rs1529641	0.83[CEU][hapmap]
rs1560569	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs1980428	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1984791	0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2012680	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012690	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012696	0.98[ASN][1000 genomes]
rs2016942	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2455603	0.85[YRI][hapmap]
rs2568020	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568021	0.92[YRI][hapmap]
rs2568043	0.85[CEU][hapmap]
rs2568045	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2568061	0.84[CEU][hapmap]
rs2568065	0.84[CEU][hapmap]
rs2568090	0.84[CEU][hapmap]
rs2653570	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2653588	0.81[YRI][hapmap]
rs2653605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742470	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2742471	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742474	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742479	0.88[YRI][hapmap]
rs2742480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742536	0.85[CEU][hapmap]
rs2742537	0.92[CEU][hapmap]
rs2742540	0.92[CEU][hapmap]
rs2742545	0.92[CEU][hapmap]
rs2742552	0.92[CEU][hapmap]
rs4909952	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4910062	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs4910156	0.81[ASN][1000 genomes]
rs4910157	0.83[EUR][1000 genomes]
rs4910200	0.84[ASN][1000 genomes]
rs4910442	0.80[CEU][hapmap]
rs4929922	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6486060	0.85[CEU][hapmap]
rs7119939	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs7123429	0.85[CEU][hapmap]
rs7479407	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7482838	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7484180	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7925728	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930026	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7937298	0.85[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap]
rs7945705	0.84[CEU][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv896984	chr11:8988550-9090408	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1980429	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs1980429	TMEM9B-AS1	cis	Thyroid	GTEx
rs1980429	TMEM9B-AS1	cis	Artery Aorta	GTEx
rs1980429	TMEM9B-AS1	cis	lung	GTEx
rs1980429	TMEM9B-AS1	cis	Artery Tibial	GTEx
rs1980429	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs1980429	TMEM9B-AS1	cis	Esophagus Mucosa	GTEx
rs1980429	TMEM9B-AS1	cis	Stomach	GTEx
rs1980429	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8987000-9011000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:8987800-9012000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr11:8989600-9011200	Weak transcription	Brain Anterior Caudate	brain
4	chr11:8989600-9019600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:8991800-9015600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:9001800-9015200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:9009600-9010800	Flanking Active TSS	K562	blood
8	chr11:9009600-9011600	Enhancers	Placenta Amnion	Placenta Amnion
9	chr11:9009800-9011800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:9010000-9011000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:9010000-9011200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:9010000-9011200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:9010000-9011600	Enhancers	Hela-S3	cervix
14	chr11:9010000-9011600	Enhancers	HSMM	muscle
15	chr11:9010000-9011800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:9010000-9011800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:9010000-9012000	Enhancers	NHLF	lung
18	chr11:9010200-9010600	Enhancers	Aorta	Aorta
19	chr11:9010200-9011000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:9010200-9011200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:9010200-9011200	Enhancers	NHEK	skin
22	chr11:9010200-9011200	Enhancers	Osteobl	bone
23	chr11:9010200-9011400	Enhancers	HMEC	breast
24	chr11:9010200-9011600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr11:9010200-9011600	Enhancers	NH-A	brain
26	chr11:9010200-9011800	Enhancers	HSMMtube	muscle
27	chr11:9010200-9011800	Enhancers	NHDF-Ad	bronchial
28	chr11:9010200-9012000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:9010400-9011000	Weak transcription	HUVEC	blood vessel
30	chr11:9010400-9011200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr11:9010400-9011200	Enhancers	A549	lung
32	chr11:9010400-9011600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:9010400-9011600	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr11:9010400-9011800	Enhancers	Primary monocytes fromperipheralblood	blood

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