Variant report

Variant	rs7928249
Chromosome Location	chr11:71161063-71161064
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	ZNF384	chr11:71160617-71161066	K562	blood:	n/a	n/a
2	TEAD4	chr11:71160695-71161169	K562	blood:	n/a	n/a
3	MYC	chr11:71160891-71161911	MCF10A-Er-Src	breast:	n/a	n/a
4	TBP	chr11:71160755-71161102	K562	blood:	n/a	n/a
5	MYC	chr11:71158869-71161077	K562	blood:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
6	MXI1	chr11:71158050-71161114	IMR90	lung:	n/a	chr11:71159719-71159728 chr11:71159721-71159730 chr11:71159719-71159728
7	ATF1	chr11:71160559-71161136	K562	blood:	n/a	n/a
8	MYC	chr11:71158882-71161096	K562	blood:	n/a	chr11:71159722-71159731 chr11:71159720-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159719-71159729 chr11:71159719-71159730 chr11:71159720-71159729 chr11:71159720-71159730
9	ARID3A	chr11:71160951-71161088	K562	blood:	n/a	n/a
10	EP300	chr11:71160561-71161127	K562	blood:	n/a	n/a
11	MXI1	chr11:71158250-71161741	SK-N-SH	brain:	n/a	chr11:71159719-71159728 chr11:71159721-71159730 chr11:71159719-71159728
12	MYC	chr11:71160935-71161071	MCF10A-Er-Src	breast:	n/a	n/a
13	RCOR1	chr11:71160720-71161102	K562	blood:	n/a	n/a
14	MXI1	chr11:71160896-71161297	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:71159116..71165503-chr11:71274687..71279227,9	MCF-7	breast:
2	chr11:71156994..71165841-chr11:71185066..71202614,31	MCF-7	breast:
3	chr11:71157940..71161417-chr11:71161465..71165970,9	K562	blood:

Variant related genes	Relation type
DHCR7	TF binding region
NADSYN1	TF binding region
ENSG00000172893	Chromatin interaction
ENSG00000204572	Chromatin interaction
ENSG00000172890	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 15 )

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

rs_ID	r²[population]
rs1044482	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11233746	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11233747	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11233789	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11546509	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11600569	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11600860	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11603330	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11604642	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11606033	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11606612	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11606631	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12278461	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12419279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12419334	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12422045	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12785878	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12789751	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12790010	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12790558	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12791871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12792306	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12793224	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12793530	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12794668	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12797951	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12800438	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12803256	0.81[ASN][1000 genomes]
rs12806844	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12806918	0.82[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap]
rs12807718	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12807827	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12808368	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1630498	0.82[TSI][hapmap]
rs1790324	0.82[TSI][hapmap]
rs1790345	0.82[TSI][hapmap]
rs1792229	0.85[TSI][hapmap]
rs1792282	0.82[TSI][hapmap]
rs1792284	0.82[TSI][hapmap]
rs1981412	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2002063	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2002064	0.85[TSI][hapmap]
rs2040323	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276360	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276361	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276362	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282620	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282621	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28364617	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2852853	0.94[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3750997	0.95[CEU][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3794060	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4423214	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4488226	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944044	0.86[CHB][hapmap]
rs4944062	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944946	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944949	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944955	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944956	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944957	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs4944958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944996	0.88[ASN][1000 genomes]
rs4945008	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs732934	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs736894	0.82[TSI][hapmap]
rs7935125	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7938885	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7944926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs909217	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7928249	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs7928249	RP11-660L16.2	cis	Whole Blood	GTEx
rs7928249	RNF121	cis	parietal	SCAN
rs7928249	NADSYN1	cis	Thyroid	GTEx
rs7928249	RP11-660L16.2	cis	Thyroid	GTEx
rs7928249	RAB6A	cis	cerebellum	SCAN
rs7928249	RP11-660L16.2	cis	Esophagus Muscularis	GTEx
rs7928249	NADSYN1	cis	lung	GTEx
rs7928249	DHCR7	cis	cerebellum	SCAN
rs7928249	NADSYN1	cis	Nerve Tibial	GTEx
rs7928249	RP11-660L16.2	cis	Adipose Subcutaneous	GTEx
rs7928249	RP11-660L16.2	cis	Artery Aorta	GTEx
rs7928249	RP11-660L16.2	cis	Nerve Tibial	GTEx
rs7928249	RP11-660L16.2	cis	Heart Left Ventricle	GTEx
rs7928249	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71158400-71161200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr11:71158400-71161200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr11:71158400-71161400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr11:71158600-71161200	Active TSS	H1 Cell Line	embryonic stem cell
5	chr11:71158600-71161200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr11:71158600-71161200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr11:71158600-71161200	Active TSS	HMEC	breast
8	chr11:71158600-71161400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr11:71158800-71161200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:71158800-71162000	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr11:71158800-71162000	Active TSS	GM12878-XiMat	blood
12	chr11:71159800-71161200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr11:71159800-71161200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:71159800-71161200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
15	chr11:71159800-71161400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:71160000-71161200	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr11:71160000-71161200	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr11:71160200-71161400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr11:71160200-71161400	Flanking Active TSS	HUVEC	blood vessel
20	chr11:71160400-71161800	Flanking Active TSS	Dnd41	blood
21	chr11:71160400-71162800	Weak transcription	Gastric	stomach
22	chr11:71160400-71163000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr11:71160600-71161200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr11:71160600-71161200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr11:71160600-71161200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr11:71160600-71161200	Flanking Active TSS	Hela-S3	cervix
27	chr11:71160600-71161400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr11:71160600-71161400	Enhancers	Liver	Liver
29	chr11:71160600-71161800	Enhancers	Adipose Nuclei	Adipose
30	chr11:71160600-71161800	Active TSS	Fetal Brain Female	brain
31	chr11:71160600-71162600	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr11:71160600-71162800	Enhancers	Primary B cells from cord blood	blood
33	chr11:71160600-71163000	Enhancers	Primary hematopoietic stem cells	blood
34	chr11:71160600-71163000	Weak transcription	Placenta	Placenta
35	chr11:71160600-71163000	Weak transcription	Left Ventricle	heart
36	chr11:71160600-71163000	Weak transcription	Right Atrium	heart
37	chr11:71160600-71163400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:71160600-71163400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr11:71160600-71163400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:71160600-71163400	Weak transcription	HSMMtube	muscle
41	chr11:71160800-71161200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr11:71160800-71161200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr11:71160800-71161200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr11:71160800-71161200	Active TSS	Muscle Satellite Cultured Cells	--
45	chr11:71160800-71161200	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr11:71160800-71161200	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr11:71160800-71161200	Active TSS	Thymus	Thymus
48	chr11:71160800-71161200	Enhancers	A549	lung
49	chr11:71160800-71161200	Enhancers	HSMM	muscle
50	chr11:71160800-71161400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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