Variant report

Variant	rs2742519
Chromosome Location	chr11:8933853-8933854
allele	A/C
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	YY1	chr11:8933776-8934159	H1-hESC	embryonic stem cell:	n/a	chr11:8933922-8933944 chr11:8933933-8933941 chr11:8933932-8933944
2	MXI1	chr11:8931149-8934261	SK-N-SH	brain:	n/a	n/a
3	ZNF384	chr11:8933021-8933934	GM12878	blood:	n/a	n/a
4	RPC155	chr11:8933241-8933970	Hela-S3	cervix:	n/a	n/a
5	ZNF384	chr11:8932558-8934324	K562	blood:	n/a	n/a
6	YY1	chr11:8933820-8934189	SK-N-SH_RA	brain:	n/a	chr11:8933922-8933944 chr11:8933933-8933941 chr11:8933932-8933944

No.	Distal block	Cell Line	Cell type
1	chr11:8930312..8934560-chr11:9023959..9026944,3	K562	blood:
2	chr11:8702257..8705886-chr11:8931185..8934379,5	MCF-7	breast:
3	chr11:8891163..8893518-chr11:8931818..8934397,2	MCF-7	breast:
4	chr11:8931659..8933906-chr11:8984325..8986430,2	K562	blood:
5	chr11:8723990..8726026-chr11:8932554..8934656,2	K562	blood:
6	chr11:8932589..8934691-chr11:10326254..10327939,2	MCF-7	breast:

Variant related genes	Relation type
ST5	TF binding region
ENSG00000200983	Chromatin interaction
ENSG00000253973	Chromatin interaction
ENSG00000166444	Chromatin interaction
ENSG00000175348	Chromatin interaction
ENSG00000166441	Chromatin interaction
ENSG00000148926	Chromatin interaction
ENSG00000175352	Chromatin interaction
ENSG00000254860	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10219366	0.83[AMR][1000 genomes]
rs1025438	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10734639	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10743094	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10769974	0.83[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10769976	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10769977	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10840150	0.81[AMR][1000 genomes]
rs10840151	0.83[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10840153	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10840154	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10840155	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10840156	0.91[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs11042128	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11042129	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11042131	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1136966	0.82[MEX][hapmap]
rs12296005	0.85[JPT][hapmap]
rs12794962	0.84[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs12798311	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1347016	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2016844	0.91[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2043218	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2056903	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2116510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2116511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2163625	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2246878	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2247038	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2316523	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2316541	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2568034	0.91[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs2568042	0.91[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap]
rs2568047	0.84[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]
rs2568069	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2568070	0.81[YRI][hapmap]
rs2568074	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568075	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568077	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568079	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2568081	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2568086	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2568087	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2568088	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2653556	0.87[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap]
rs2653565	0.91[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs2653590	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2653594	0.89[EUR][1000 genomes]
rs2653597	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2653601	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2653604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2653611	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2742486	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2742487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2742488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2742489	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2742491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2742493	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2742494	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2742495	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2742496	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[ASN][1000 genomes]
rs2742497	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2742502	0.82[MEX][hapmap]
rs2742504	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2742505	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2742512	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742513	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742521	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs3751063	0.91[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3751065	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3751066	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3751068	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3763911	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3763912	0.83[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4370967	0.84[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs4909951	0.91[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7106152	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72851596	0.93[ASN][1000 genomes]
rs72852790	0.88[ASN][1000 genomes]
rs72853712	0.88[ASN][1000 genomes]
rs7932377	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7940895	0.81[ASN][1000 genomes]
rs7942026	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7951226	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs909464	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9300096	0.91[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs982273	0.87[CEU][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2742519	TMEM9B	cis	parietal	SCAN
rs2742519	C11orf17	cis	lymphoblastoid	seeQTL
rs2742519	C11orf17	cis	multi-tissue	Pritchard
rs2742519	MRVI1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8931400-8934000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr11:8931400-8934000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:8931400-8934000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:8931400-8934000	Active TSS	Rectal Smooth Muscle	rectum
5	chr11:8931400-8934200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:8931600-8934000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:8931600-8934000	Active TSS	Colonic Mucosa	Colon
8	chr11:8931600-8934000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr11:8931600-8934000	Active TSS	Ovary	ovary
10	chr11:8931600-8934000	Active TSS	Right Atrium	heart
11	chr11:8931600-8934400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr11:8931600-8935200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:8931800-8934000	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr11:8931800-8934000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:8931800-8934000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr11:8931800-8934000	Active TSS	HSMM	muscle
17	chr11:8931800-8934000	Active TSS	HSMMtube	muscle
18	chr11:8931800-8934200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:8931800-8934200	Active TSS	Fetal Brain Female	brain
20	chr11:8931800-8934200	Active TSS	Fetal Kidney	kidney
21	chr11:8931800-8934200	Active TSS	Thymus	Thymus
22	chr11:8931800-8934400	Active TSS	Brain Substantia Nigra	brain
23	chr11:8932000-8934000	Active TSS	H1 Cell Line	embryonic stem cell
24	chr11:8932000-8934000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr11:8932000-8934000	Active TSS	Fetal Intestine Large	intestine
26	chr11:8932000-8934000	Active TSS	Fetal Muscle Trunk	muscle
27	chr11:8932000-8934000	Active TSS	Psoas Muscle	Psoas
28	chr11:8932000-8934000	Active TSS	NHDF-Ad	bronchial
29	chr11:8932000-8934200	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr11:8932000-8934400	Active TSS	GM12878-XiMat	blood
31	chr11:8932200-8934000	Active TSS	Fetal Intestine Small	intestine
32	chr11:8932200-8934000	Active TSS	NH-A	brain
33	chr11:8932200-8934400	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr11:8932200-8934400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:8932200-8934400	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr11:8932400-8934000	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr11:8932400-8934000	Active TSS	HMEC	breast
38	chr11:8932800-8934000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr11:8932800-8934000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr11:8932800-8934000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr11:8933000-8934200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:8933000-8934200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:8933000-8934200	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr11:8933200-8934000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr11:8933200-8934000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr11:8933200-8934200	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr11:8933400-8934000	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr11:8933400-8934000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr11:8933400-8934200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr11:8933400-8934400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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