Variant report

Variant	rs10769979
Chromosome Location	chr11:9010659-9010660
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	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
2	SMARCB1	chr11:9009830-9010745	K562	blood:	n/a	chr11:9010386-9010395
3	TEAD4	chr11:9009771-9011748	K562	blood:	n/a	n/a
4	TEAD4	chr11:9009765-9010691	K562	blood:	n/a	n/a
5	TRIM28	chr11:9009773-9010679	K562	blood:	n/a	n/a
6	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
7	UBTF	chr11:9009886-9010746	K562	blood:	n/a	n/a
8	NR2F2	chr11:9009737-9010726	K562	blood:	n/a	n/a
9	GATA1	chr11:9009690-9010922	PBDE	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
10	ARID3A	chr11:9009838-9010684	K562	blood:	n/a	chr11:9010619-9010635

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: 74 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10743093	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs10743095	0.84[EUR][1000 genomes]
rs10769967	0.93[CEU][hapmap]
rs10769970	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs10769971	0.87[JPT][hapmap];1.00[YRI][hapmap]
rs10769973	0.93[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs10769978	0.86[EUR][1000 genomes]
rs10769980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769981	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10840130	0.84[CEU][hapmap]
rs10840134	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10840141	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10840142	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs10840147	0.89[ASW][hapmap];0.89[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs10840148	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs10840157	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840158	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840160	0.83[CHD][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs11042078	0.89[CEU][hapmap]
rs11042103	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11042125	0.89[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11042149	0.89[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs11042150	0.82[EUR][1000 genomes]
rs11042151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap]
rs11042152	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042154	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1109305	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1123936	0.93[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs11603841	0.88[CEU][hapmap]
rs1529641	0.91[CEU][hapmap]
rs1560569	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs1980428	0.93[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs1980429	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]
rs1984791	0.83[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs2012680	0.96[ASN][1000 genomes]
rs2012690	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2012696	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2016942	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2568020	0.98[ASN][1000 genomes]
rs2568043	0.92[CEU][hapmap]
rs2568045	0.93[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2568061	0.93[CEU][hapmap];0.91[MEX][hapmap]
rs2568065	0.93[CEU][hapmap];0.91[MEX][hapmap]
rs2568090	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs2653570	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.98[ASN][1000 genomes]
rs2653605	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.98[ASN][1000 genomes]
rs2742470	0.82[EUR][1000 genomes]
rs2742471	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742474	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2742480	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2742537	0.83[CEU][hapmap]
rs2742540	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs2742545	0.85[CEU][hapmap]
rs2742552	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs4909952	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4910062	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs4910156	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4910158	0.83[EUR][1000 genomes]
rs4910200	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4910442	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs4929922	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6486060	0.92[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs7119939	0.92[CEU][hapmap]
rs7123429	0.93[CEU][hapmap]
rs7479407	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7482838	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7484180	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7925728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7937298	0.93[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs7945705	0.93[CEU][hapmap];0.82[JPT][hapmap];0.82[MEX][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10769979	TMEM9B-AS1	cis	lung	GTEx
rs10769979	AKIP1	cis	Thyroid	GTEx
rs10769979	RRP8	cis	parietal	SCAN
rs10769979	OR52A1	cis	parietal	SCAN
rs10769979	C11orf17	cis	multi-tissue	Pritchard
rs10769979	RPL27A	cis	parietal	SCAN
rs10769979	TMEM9B	cis	parietal	SCAN
rs10769979	APBB1	cis	parietal	SCAN
rs10769979	NRIP3	cis	parietal	SCAN
rs10769979	ST5	cis	parietal	SCAN
rs10769979	WEE1	cis	parietal	SCAN

Chromatin state (count:35 , 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	chr11:9010200-9011000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:9010200-9011200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:9010200-9011200	Enhancers	NHEK	skin
21	chr11:9010200-9011200	Enhancers	Osteobl	bone
22	chr11:9010200-9011400	Enhancers	HMEC	breast
23	chr11:9010200-9011600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr11:9010200-9011600	Enhancers	NH-A	brain
25	chr11:9010200-9011800	Enhancers	HSMMtube	muscle
26	chr11:9010200-9011800	Enhancers	NHDF-Ad	bronchial
27	chr11:9010200-9012000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:9010400-9011000	Weak transcription	HUVEC	blood vessel
29	chr11:9010400-9011200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr11:9010400-9011200	Enhancers	A549	lung
31	chr11:9010400-9011600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:9010400-9011600	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr11:9010400-9011800	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr11:9010600-9010800	Weak transcription	Aorta	Aorta
35	chr11:9010600-9011600	Enhancers	Monocytes-CD14+_RO01746	blood

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