Variant report

Variant	rs11600569
Chromosome Location	chr11:71173747-71173748
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:71171741..71174523-chr11:71191219..71193247,2	MCF-7	breast:
2	chr11:71173517..71174399-chr11:71192570..71193116,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172890	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1044482	0.95[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11233746	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11233747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11233789	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11546509	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11600860	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11603330	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11604642	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11606033	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11606612	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11606631	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12278461	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12419279	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12419334	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12422045	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12785878	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12789751	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12790010	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12791871	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12792306	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12793224	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12793530	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12794668	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12797951	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12800438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12806844	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12807718	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12807827	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12808368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1981412	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2002063	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2040323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276360	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276361	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282620	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2282621	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28364617	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2852853	0.94[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3750997	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs3794060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4423214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4488226	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944044	0.82[CHB][hapmap]
rs4944062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944946	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4944949	0.92[ASN][1000 genomes]
rs4944955	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944956	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944957	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4944958	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944959	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944996	0.90[ASN][1000 genomes]
rs4945008	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs732934	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7928249	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7935125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7944926	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs909217	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv1052432	chr11:71167449-71213007	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs11600569	RP11-660L16.2	cis	Heart Left Ventricle	GTEx
rs11600569	RP11-660L16.2	cis	Stomach	GTEx
rs11600569	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs11600569	RP11-660L16.2	cis	Thyroid	GTEx
rs11600569	RP11-660L16.2	cis	Adipose Subcutaneous	GTEx
rs11600569	RP11-660L16.2	cis	Nerve Tibial	GTEx
rs11600569	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11600569	RP11-660L16.2	cis	Artery Aorta	GTEx
rs11600569	NADSYN1	cis	Thyroid	GTEx
rs11600569	RP11-660L16.2	cis	Whole Blood	GTEx
rs11600569	RP11-660L16.2	cis	Esophagus Muscularis	GTEx
rs11600569	NADSYN1	cis	Nerve Tibial	GTEx
rs11600569	NADSYN1	cis	Artery Tibial	GTEx
rs11600569	NADSYN1	cis	lung	GTEx
rs11600569	RP11-660L16.2	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71165000-71210000	Weak transcription	Psoas Muscle	Psoas
2	chr11:71165200-71177400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:71165200-71177600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:71165200-71199200	Weak transcription	Right Atrium	heart
5	chr11:71165400-71194200	Weak transcription	Fetal Heart	heart
6	chr11:71165800-71174000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr11:71165800-71175800	Strong transcription	Fetal Muscle Trunk	muscle
8	chr11:71165800-71178200	Strong transcription	NHLF	lung
9	chr11:71165800-71178400	Strong transcription	Fetal Stomach	stomach
10	chr11:71165800-71179200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:71165800-71179200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:71165800-71179200	Strong transcription	Fetal Muscle Leg	muscle
13	chr11:71165800-71180400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr11:71165800-71218400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr11:71166000-71173800	Strong transcription	Brain Substantia Nigra	brain
16	chr11:71166000-71175400	Strong transcription	Brain Cingulate Gyrus	brain
17	chr11:71166000-71175600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr11:71166000-71176000	Strong transcription	Brain Anterior Caudate	brain
19	chr11:71166000-71178400	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr11:71166000-71178600	Strong transcription	Primary T cells from cord blood	blood
21	chr11:71166000-71178600	Strong transcription	Spleen	Spleen
22	chr11:71166000-71179200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr11:71166000-71180000	Strong transcription	A549	lung
24	chr11:71166000-71180200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr11:71166000-71180200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr11:71166000-71194200	Weak transcription	Fetal Brain Male	brain
27	chr11:71166200-71173800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:71166200-71175200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr11:71166200-71175200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:71166200-71175200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:71166200-71175200	Strong transcription	Right Ventricle	heart
32	chr11:71166200-71175200	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr11:71166200-71175400	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr11:71166200-71175600	Strong transcription	Fetal Thymus	thymus
35	chr11:71166200-71175800	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr11:71166200-71178000	Strong transcription	Aorta	Aorta
37	chr11:71166200-71178000	Strong transcription	Fetal Intestine Small	intestine
38	chr11:71166200-71178400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:71166200-71178400	Strong transcription	Thymus	Thymus
40	chr11:71166200-71178600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr11:71166200-71178600	Strong transcription	Lung	lung
42	chr11:71166200-71178600	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr11:71166200-71178800	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr11:71166200-71178800	Strong transcription	Stomach Smooth Muscle	stomach
45	chr11:71166200-71179000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr11:71166200-71179000	Strong transcription	Adipose Nuclei	Adipose
47	chr11:71166200-71179400	Strong transcription	Liver	Liver
48	chr11:71166200-71179600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr11:71166200-71179800	Strong transcription	Primary B cells from cord blood	blood
50	chr11:71166200-71180000	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links