Variant report

Variant	rs2174162
Chromosome Location	chr11:16419949-16419950
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	chr11:16419460..16421100-chr11:16436928..16438433,2	K562	blood:
2	chr11:16419446..16421077-chr11:16594061..16596211,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1018143	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10766320	0.99[ASN][1000 genomes]
rs10766321	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10766322	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10766323	0.82[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10832598	0.98[ASN][1000 genomes]
rs10832599	0.99[ASN][1000 genomes]
rs10832600	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832605	0.82[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10832606	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10832608	0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs11023944	0.82[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs11023945	0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11820804	0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12277548	0.82[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs12800228	0.98[ASN][1000 genomes]
rs1503447	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1503448	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1503449	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1875717	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1910406	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1910407	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2089050	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2134609	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2174163	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs297324	0.82[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap]
rs297326	0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs297333	0.99[ASN][1000 genomes]
rs297334	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs297339	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.81[YRI][hapmap];0.99[ASN][1000 genomes]
rs61881798	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs626927	0.85[JPT][hapmap]
rs7121140	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7925322	0.99[ASN][1000 genomes]
rs7929425	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7929629	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7932314	0.99[ASN][1000 genomes]
rs7942989	0.99[ASN][1000 genomes]
rs7945277	0.86[ASN][1000 genomes]
rs7951214	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.99[ASN][1000 genomes]
rs957476	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529731	chr11:16122782-16468170	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv553566	chr11:16329009-16799044	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv832075	chr11:16391700-16490934	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2174162	C11orf58	cis	cerebellum	SCAN
rs2174162	RP1-239B22.5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16415400-16424400	Weak transcription	Fetal Heart	heart
2	chr11:16417200-16434200	Weak transcription	Psoas Muscle	Psoas
3	chr11:16418000-16425200	Weak transcription	Brain Germinal Matrix	brain
4	chr11:16418800-16420200	Enhancers	HepG2	liver
5	chr11:16419200-16420400	Enhancers	Fetal Intestine Large	intestine
6	chr11:16419200-16420400	Enhancers	Fetal Intestine Small	intestine
7	chr11:16419400-16420200	Enhancers	Small Intestine	intestine
8	chr11:16419600-16423600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:16419600-16424000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:16419600-16424000	Weak transcription	Brain Anterior Caudate	brain
11	chr11:16419600-16425000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr11:16419800-16423600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:16419800-16423800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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