Variant report

Variant	rs1980428
Chromosome Location	chr11:9010497-9010498
allele	A/G
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	FOS	chr11:9010190-9010557	K562	blood:	n/a	chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010386-9010394 chr11:9010385-9010395
10	MYC	chr11:9009854-9010526	K562	blood:	n/a	n/a
11	POLR2A	chr11:9010119-9010568	K562	blood:	n/a	n/a
12	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
13	SMARCB1	chr11:9009830-9010745	K562	blood:	n/a	chr11:9010386-9010395
14	TBP	chr11:9010267-9010509	K562	blood:	n/a	n/a
15	BHLHE40	chr11:9009989-9010608	K562	blood:	n/a	n/a
16	MAX	chr11:9010043-9010612	K562	blood:	n/a	n/a
17	RCOR1	chr11:9009812-9010638	K562	blood:	n/a	n/a
18	IRF1	chr11:9009884-9010619	K562	blood:	n/a	n/a
19	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
20	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
21	STAT5A	chr11:9009786-9010635	K562	blood:	n/a	n/a
22	EP300	chr11:9009861-9010612	K562	blood:	n/a	n/a
23	TBL1XR1	chr11:9009946-9010610	K562	blood:	n/a	n/a
24	TEAD4	chr11:9009771-9011748	K562	blood:	n/a	n/a
25	PML	chr11:9009843-9010607	K562	blood:	n/a	n/a
26	PML	chr11:9009771-9010635	K562	blood:	n/a	n/a
27	MAZ	chr11:9009992-9010557	K562	blood:	n/a	n/a
28	HDAC2	chr11:9009829-9010595	K562	blood:	n/a	chr11:9010141-9010155
29	ATF3	chr11:9010135-9010595	K562	blood:	n/a	n/a
30	CCNT2	chr11:9009733-9010551	K562	blood:	n/a	chr11:9010330-9010350
31	HDAC2	chr11:9010157-9010580	K562	blood:	n/a	n/a
32	TEAD4	chr11:9009765-9010691	K562	blood:	n/a	n/a
33	E2F6	chr11:9010310-9010531	K562	blood:	n/a	n/a
34	POLR2A	chr11:9009750-9010654	K562	blood:	n/a	n/a
35	NR2F2	chr11:9009827-9010569	K562	blood:	n/a	n/a
36	TRIM28	chr11:9009773-9010679	K562	blood:	n/a	n/a
37	ZNF143	chr11:9010034-9010502	K562	blood:	n/a	n/a
38	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
39	MAFK	chr11:9010293-9010588	IMR90	lung:	n/a	n/a
40	STAT5A	chr11:9009803-9010599	K562	blood:	n/a	n/a
41	CBX3	chr11:9009915-9010632	K562	blood:	n/a	n/a
42	ZNF274	chr11:9010037-9010506	K562	blood:	n/a	n/a
43	POLR2A	chr11:9009863-9010539	K562	blood:	n/a	n/a
44	MAFF	chr11:9009908-9010598	K562	blood:	n/a	n/a
45	JUN	chr11:9010020-9010633	K562	blood:	n/a	chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010386-9010394 chr11:9010385-9010395
46	EP300	chr11:9009931-9010512	K562	blood:	n/a	n/a
47	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
48	FOS	chr11:9010284-9010545	MCF10A-Er-Src	breast:	n/a	chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010386-9010394 chr11:9010385-9010395
49	UBTF	chr11:9009886-9010746	K562	blood:	n/a	n/a
50	NR2F2	chr11:9009737-9010726	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:9010492-9010542	HCF	heart:	n/a
2	chr11:9010492-9010542	HRE	kidney:	n/a
3	chr11:9010492-9010542	HIPEpiC	eye:	n/a
4	chr11:9010492-9010542	RPTEC	kidney:	n/a
5	chr11:9010492-9010542	H1-hESC	embryonic stem cell:	embryo
6	chr11:9010492-9010542	HMEC	breast:	n/a
7	chr11:9010492-9010542	Hepatocyte	liver:	n/a
8	chr11:9010492-9010542	Jurkat	blood:	n/a
9	chr11:9010492-9010542	BE2_C	brain:	n/a
10	chr11:9010492-9010542	NB4	blood:	n/a
11	chr11:9010492-9010542	GM12878	blood:	n/a
12	chr11:9010492-9010542	HCT-116	colon:	n/a
13	chr11:9010492-9010542	NH-A	brain:	n/a
14	chr11:9010492-9010542	MCF10A-Er-Src	breast:	n/a
15	chr11:9010492-9010542	LNCaP	prostate:	n/a
16	chr11:9010492-9010542	HL-60	blood:	n/a
17	chr11:9010492-9010542	AG10803	skin:	n/a
18	chr11:9010492-9010542	AG04450	lung:	fetal
19	chr11:9010492-9010542	HCPEpiC	choroid plexus:	n/a
20	chr11:9010492-9010542	HNPCEpiC	eye:	n/a
21	chr11:9010492-9010542	SKMC	muscle:	n/a
22	chr11:9010492-9010542	SK-N-SH_RA	brain:	n/a
23	chr11:9010492-9010542	HPAEpiC	pulmonary alveolar:	n/a
24	chr11:9010492-9010542	GM06990	blood:	n/a
25	chr11:9010492-9010542	GM19239	blood:	n/a
26	chr11:9010492-9010542	NHDF-neo	bronchial:	n/a
27	chr11:9010492-9010542	NT2-D1	testis:	n/a
28	chr11:9010492-9010542	BJ	skin:	n/a
29	chr11:9010492-9010542	U87	brain:	n/a
30	chr11:9010492-9010542	AoSMC	blood vessel:	n/a
31	chr11:9010492-9010542	Caco-2	colon:	n/a
32	chr11:9010492-9010542	SAEC	small airway:	n/a
33	chr11:9010492-9010542	GM12891	blood:	n/a
34	chr11:9010492-9010542	SK-N-MC	brain:	n/a
35	chr11:9010492-9010542	SK-N-SH	brain:	n/a
36	chr11:9010492-9010542	HAEpiC	amniotic membrane:	n/a
37	chr11:9010492-9010542	A549	lung:	n/a
38	chr11:9010492-9010542	ovcar-3	ovarian:	n/a
39	chr11:9010492-9010542	HCM	heart:	n/a
40	chr11:9010492-9010542	CMK	blood:	n/a
41	chr11:9010492-9010542	PFSK-1	brain:	n/a
42	chr11:9010492-9010542	HRPEpiC	eye:	n/a
43	chr11:9010492-9010542	AG04449	skin:	fetal
44	chr11:9010492-9010542	HepG2	liver:	n/a
45	chr11:9010492-9010542	ECC-1	luminal epithelium:	n/a
46	chr11:9010492-9010542	GM12892	blood:	n/a
47	chr11:9010492-9010542	HUVEC	blood vessel:	n/a
48	chr11:9010492-9010542	PANC-1	pancreas:	n/a
49	chr11:9010492-9010542	T-47D	breast:	n/a
50	chr11:9010492-9010542	MCF-7	breast:	n/a

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
NRIP3	CpG island
ENSG00000253973	Chromatin interaction
ENSG00000175352	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10743093	0.84[CEU][hapmap]
rs10769967	0.85[CEU][hapmap]
rs10769970	0.85[CEU][hapmap]
rs10769973	0.85[CEU][hapmap]
rs10769979	0.93[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs10769980	0.83[EUR][1000 genomes]
rs10840134	0.84[CEU][hapmap]
rs10840135	0.83[JPT][hapmap]
rs10840141	0.85[CEU][hapmap]
rs10840142	0.85[CEU][hapmap]
rs10840147	0.89[CEU][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap]
rs10840148	0.85[CEU][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap]
rs10840158	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11042078	0.81[CEU][hapmap]
rs11042103	0.85[CEU][hapmap]
rs11042104	0.83[JPT][hapmap]
rs11042125	0.85[CEU][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap]
rs11042149	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042150	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11042151	0.93[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs11042152	0.82[EUR][1000 genomes]
rs11042154	0.93[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs1123936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603841	0.87[CEU][hapmap]
rs1368017	0.83[JPT][hapmap]
rs1529641	0.82[CEU][hapmap]
rs1560569	0.93[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap]
rs16906256	0.83[JPT][hapmap]
rs1980429	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2012680	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2012690	0.96[EUR][1000 genomes]
rs2016942	0.93[CEU][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap]
rs2568020	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2568043	0.84[CEU][hapmap]
rs2568045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568061	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap]
rs2568065	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap]
rs2568090	0.85[CEU][hapmap]
rs2653570	0.96[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2653605	1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2742470	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742471	0.82[EUR][1000 genomes]
rs2742474	0.82[EUR][1000 genomes]
rs2742480	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2742536	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap]
rs2742537	0.91[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap]
rs2742540	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap]
rs2742545	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2742552	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap]
rs4909952	0.92[CEU][hapmap]
rs4910062	0.83[CEU][hapmap]
rs4910157	0.83[EUR][1000 genomes]
rs4910442	0.84[CEU][hapmap]
rs4929922	0.90[GIH][hapmap];0.82[MEX][hapmap]
rs6486060	0.85[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7119939	0.84[CEU][hapmap]
rs7123429	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap]
rs7479407	0.93[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs7482838	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7925728	0.93[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7930026	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7937298	0.85[CEU][hapmap]
rs7945705	0.85[CEU][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1980428	RRP8	cis	parietal	SCAN
rs1980428	NRIP3	cis	parietal	SCAN
rs1980428	TMEM9B-AS1	cis	lung	GTEx
rs1980428	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs1980428	OR52A1	cis	parietal	SCAN
rs1980428	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs1980428	RPL27A	cis	parietal	SCAN
rs1980428	TMEM9B-AS1	cis	Thyroid	GTEx
rs1980428	C11orf17	cis	multi-tissue	Pritchard
rs1980428	TMEM9B-AS1	cis	Esophagus Mucosa	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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