Variant report

Variant	rs11165364
Chromosome Location	chr1:91841637-91841638
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:91840019..91844742-chr1:91867807..91870746,5	K562	blood:

Variant related genes	Relation type
ENSG00000162669	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10493846	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs10801861	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs10923009	0.81[EUR][1000 genomes]
rs11164779	0.90[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11165744	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs11165778	0.90[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs1158437	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs11584478	0.95[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs11588502	0.83[EUR][1000 genomes]
rs11589490	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs12060327	0.90[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.81[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12080491	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs12094120	0.85[EUR][1000 genomes]
rs1978902	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs1978903	0.95[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2083450	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs2119251	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs28445469	0.85[EUR][1000 genomes]
rs4512702	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs56110253	0.80[EUR][1000 genomes]
rs56355433	0.82[EUR][1000 genomes]
rs56382425	0.81[EUR][1000 genomes]
rs9324415	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs9701353	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]

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	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv1800676	chr1:91722083-91854389	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv1796351	chr1:91722083-91872374	Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv871685	chr1:91774458-91849219	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv546806	chr1:91780408-91875505	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11165364	CCDC18	cis	parietal	SCAN
rs11165364	HFM1	cis	brain	BrainEAC

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:91819400-91845200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr1:91820600-91842000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:91822800-91849000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:91824800-91852600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:91825000-91852600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:91829800-91852600	Weak transcription	Brain Germinal Matrix	brain
7	chr1:91832000-91852600	Weak transcription	Fetal Heart	heart
8	chr1:91833000-91852600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:91833000-91852600	Weak transcription	Fetal Stomach	stomach
10	chr1:91836800-91852600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:91837200-91846000	Weak transcription	Psoas Muscle	Psoas
12	chr1:91839000-91852600	Weak transcription	Fetal Intestine Large	intestine
13	chr1:91839800-91846600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:91840400-91852600	Weak transcription	Fetal Kidney	kidney
15	chr1:91840600-91852600	Weak transcription	Ovary	ovary
16	chr1:91840800-91852600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:91840800-91852600	Weak transcription	Fetal Brain Male	brain
18	chr1:91840800-91852600	Weak transcription	Fetal Lung	lung
19	chr1:91841200-91843000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:91841200-91847400	Weak transcription	Left Ventricle	heart
21	chr1:91841400-91852600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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