Variant report

Variant	rs1792315
Chromosome Location	chr11:71165547-71165548
allele	C/T
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	CTCF	chr11:71165500-71165650	GM12868	blood:	n/a	n/a

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	chr11:71156994..71165841-chr11:71185066..71202614,31	MCF-7	breast:
4	chr11:71163473..71165824-chr11:71289975..71292795,2	MCF-7	breast:

Variant related genes	Relation type
NADSYN1	TF binding region
DHCR7	TF binding region
ENSG00000172890	Chromatin interaction
ENSG00000249387	Chromatin interaction
ENSG00000172893	Chromatin interaction
ENSG00000254682	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10898144	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1123007	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12224205	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1540127	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1619577	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1629220	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1630498	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1790324	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1790328	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1790330	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1790339	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790340	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1790341	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790343	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790344	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790345	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1790350	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1790353	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1792224	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1792226	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1792227	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1792229	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1792231	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1792233	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1792234	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1792235	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1792264	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1792277	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1792280	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1792281	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1792282	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1792283	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1792284	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2002064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017686	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276358	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2511010	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3794057	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4402322	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4435028	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4616066	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs736894	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1792315	RP11-660L16.2	cis	Thyroid	GTEx
rs1792315	RP11-660L16.2	cis	Whole Blood	GTEx
rs1792315	NADSYN1	cis	Nerve Tibial	GTEx
rs1792315	RP11-660L16.2	cis	Esophagus Muscularis	GTEx
rs1792315	RP11-660L16.2	cis	Artery Aorta	GTEx
rs1792315	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs1792315	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	chr11:71163000-71165800	Active TSS	Rectal Smooth Muscle	rectum
2	chr11:71164000-71165800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:71164400-71165800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:71164600-71165800	Flanking Active TSS	Dnd41	blood
5	chr11:71164800-71165600	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr11:71164800-71165800	Flanking Active TSS	Fetal Intestine Large	intestine
7	chr11:71164800-71165800	Enhancers	Spleen	Spleen
8	chr11:71164800-71166000	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr11:71164800-71166000	Enhancers	Fetal Brain Male	brain
10	chr11:71165000-71165600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:71165000-71165800	Enhancers	Left Ventricle	heart
12	chr11:71165000-71165800	Enhancers	Placenta Amnion	Placenta Amnion
13	chr11:71165000-71165800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr11:71165000-71166000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr11:71165000-71166000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr11:71165000-71166000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr11:71165000-71166200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:71165000-71166200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr11:71165000-71210000	Weak transcription	Psoas Muscle	Psoas
20	chr11:71165200-71165600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr11:71165200-71165600	Enhancers	Primary hematopoietic stem cells	blood
22	chr11:71165200-71165600	Enhancers	Brain Angular Gyrus	brain
23	chr11:71165200-71165600	Weak transcription	Esophagus	oesophagus
24	chr11:71165200-71165600	Enhancers	Fetal Muscle Leg	muscle
25	chr11:71165200-71165800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr11:71165200-71165800	Enhancers	Primary T cells from cord blood	blood
27	chr11:71165200-71165800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:71165200-71165800	Enhancers	Fetal Brain Female	brain
29	chr11:71165200-71165800	Weak transcription	Fetal Stomach	stomach
30	chr11:71165200-71165800	Weak transcription	K562	blood
31	chr11:71165200-71165800	Enhancers	NH-A	brain
32	chr11:71165200-71166000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:71165200-71166000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr11:71165200-71166000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:71165200-71166000	Enhancers	Primary B cells from cord blood	blood
36	chr11:71165200-71166000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr11:71165200-71166000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr11:71165200-71166000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr11:71165200-71166000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:71165200-71166000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:71165200-71166000	Enhancers	Liver	Liver
42	chr11:71165200-71166000	Weak transcription	Brain Anterior Caudate	brain
43	chr11:71165200-71166000	Enhancers	Brain Hippocampus Middle	brain
44	chr11:71165200-71166000	Enhancers	Colon Smooth Muscle	Colon
45	chr11:71165200-71166000	Enhancers	Gastric	stomach
46	chr11:71165200-71166000	Enhancers	Thymus	Thymus
47	chr11:71165200-71166200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr11:71165200-71166200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr11:71165200-71166200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr11:71165200-71166200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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