Variant report

Variant	rs11546509
Chromosome Location	chr11:71162785-71162786
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POU2F2	chr11:71162781-71163191	GM12891	blood:	n/a	chr11:71162996-71163009
2	MAZ	chr11:71162507-71163273	K562	blood:	n/a	n/a
3	POU2F2	chr11:71162754-71163321	GM12878	blood:	n/a	chr11:71162996-71163009
4	USF1	chr11:71162677-71162974	H1-hESC	embryonic stem cell:	n/a	n/a
5	CUX1	chr11:71162632-71163035	K562	blood:	n/a	n/a
6	CEBPB	chr11:71162765-71163144	K562	blood:	n/a	n/a
7	USF1	chr11:71162580-71163098	H1-hESC	embryonic stem cell:	n/a	n/a
8	POU2F2	chr11:71162736-71163231	GM12891	blood:	n/a	chr11:71162996-71163009
9	RCOR1	chr11:71162761-71162879	GM12878	blood:	n/a	n/a
10	RCOR1	chr11:71162783-71163253	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:71157940..71161417-chr11:71161465..71165970,9	K562	blood:
2	chr11:71162324..71166430-chr11:71186520..71190924,4	K562	blood:
3	chr11:71159116..71165503-chr11:71274687..71279227,9	MCF-7	breast:
4	chr11:71156994..71165841-chr11:71185066..71202614,31	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NADSYN1-1	chr11:71162736-71163182	XLOC_009199
2	lnc-NADSYN1-1	chr11:71162736-71163203	ENSG00000254682.1
3	lnc-NADSYN1-1	chr11:71162736-71164062	NONHSAT022678

No data

Variant related genes	Relation type
DHCR7	TF binding region
NADSYN1	TF binding region
ENSG00000172890	Chromatin interaction
ENSG00000204572	Chromatin interaction
ENSG00000172893	Chromatin interaction
ENSG00000254682	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1044482	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11233746	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11233747	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11233789	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11600569	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11600860	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11603330	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11604642	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11606033	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11606612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606631	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12278461	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12419279	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12419334	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12422045	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12785878	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12789751	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790010	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12790558	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12791871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12792306	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12793224	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12793530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12794668	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12797951	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12800438	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12803256	0.80[ASN][1000 genomes]
rs12806844	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12807718	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12807827	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12808368	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1981412	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2002063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040323	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276360	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276361	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276362	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282620	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282621	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28364617	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2852853	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3750997	0.90[EUR][1000 genomes]
rs3794060	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4423214	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4488226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944062	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944946	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944949	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944955	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944956	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944958	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944959	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944996	0.89[ASN][1000 genomes]
rs4945008	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs732934	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7928249	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7935125	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7938885	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7944926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909217	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv1037357	chr11:71162241-71209628	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv541085	chr11:71162241-71209628	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11546509	RP11-660L16.2	cis	Nerve Tibial	GTEx
rs11546509	RP11-660L16.2	cis	Artery Aorta	GTEx
rs11546509	NADSYN1	cis	Nerve Tibial	GTEx
rs11546509	RP11-660L16.2	cis	Thyroid	GTEx
rs11546509	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs11546509	RP11-660L16.2	cis	Esophagus Muscularis	GTEx
rs11546509	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11546509	RP11-660L16.2	cis	lung	GTEx
rs11546509	NADSYN1	cis	lung	GTEx
rs11546509	RP11-660L16.2	cis	Heart Left Ventricle	GTEx
rs11546509	RP11-660L16.2	cis	Stomach	GTEx
rs11546509	RP11-660L16.2	cis	Adipose Subcutaneous	GTEx
rs11546509	RP11-660L16.2	cis	Whole Blood	GTEx
rs11546509	NADSYN1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71160400-71162800	Weak transcription	Gastric	stomach
2	chr11:71160400-71163000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:71160600-71162800	Enhancers	Primary B cells from cord blood	blood
4	chr11:71160600-71163000	Enhancers	Primary hematopoietic stem cells	blood
5	chr11:71160600-71163000	Weak transcription	Placenta	Placenta
6	chr11:71160600-71163000	Weak transcription	Left Ventricle	heart
7	chr11:71160600-71163000	Weak transcription	Right Atrium	heart
8	chr11:71160600-71163400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:71160600-71163400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr11:71160600-71163400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:71160600-71163400	Weak transcription	HSMMtube	muscle
12	chr11:71160800-71162800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:71160800-71162800	Weak transcription	Right Ventricle	heart
14	chr11:71160800-71163000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:71160800-71163000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:71160800-71163000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:71160800-71163000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr11:71160800-71163000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:71160800-71163000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr11:71160800-71163000	Weak transcription	Esophagus	oesophagus
21	chr11:71160800-71163000	Weak transcription	Fetal Heart	heart
22	chr11:71160800-71163000	Weak transcription	Pancreas	Pancrea
23	chr11:71160800-71163000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr11:71160800-71163000	Weak transcription	Stomach Mucosa	stomach
25	chr11:71160800-71163000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr11:71160800-71163200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:71160800-71163200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:71160800-71163400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr11:71160800-71163400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr11:71160800-71163400	Enhancers	Fetal Intestine Small	intestine
31	chr11:71160800-71163400	Weak transcription	Ovary	ovary
32	chr11:71160800-71163600	Weak transcription	Aorta	Aorta
33	chr11:71161000-71162800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr11:71161000-71162800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr11:71161000-71162800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:71161000-71162800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr11:71161000-71162800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr11:71161000-71162800	Weak transcription	Small Intestine	intestine
39	chr11:71161000-71163000	Enhancers	Brain Cingulate Gyrus	brain
40	chr11:71161000-71163000	Weak transcription	Colonic Mucosa	Colon
41	chr11:71161000-71163000	Weak transcription	Colon Smooth Muscle	Colon
42	chr11:71161000-71163000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr11:71161000-71163000	Weak transcription	Psoas Muscle	Psoas
44	chr11:71161000-71163200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:71161000-71163200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:71161000-71163200	Enhancers	NHEK	skin
47	chr11:71161000-71163400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr11:71161000-71163400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:71161000-71163400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr11:71161000-71163400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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