Variant report

Variant	rs11927913
Chromosome Location	chr3:160387940-160387941
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	chr3:160387401..160389689-chr3:160399672..160401960,2	K562	blood:
2	chr3:160379485..160381403-chr3:160384390..160388251,3	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10936207	0.87[ASN][1000 genomes]
rs10936208	0.86[ASN][1000 genomes]
rs10936209	0.87[ASN][1000 genomes]
rs10936210	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712392	0.82[EUR][1000 genomes]
rs11713230	0.82[EUR][1000 genomes]
rs11714916	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12490985	0.82[ASN][1000 genomes]
rs13065269	0.82[EUR][1000 genomes]
rs13074231	0.82[EUR][1000 genomes]
rs13095931	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1317085	0.87[ASN][1000 genomes]
rs1403045	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1522285	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831337	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236586	0.87[ASN][1000 genomes]
rs1879797	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1980277	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141668	0.81[EUR][1000 genomes]
rs2178451	0.81[EUR][1000 genomes]
rs2178452	0.87[ASN][1000 genomes]
rs2367209	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28544045	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28730907	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34362576	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34949451	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35008770	0.81[EUR][1000 genomes]
rs35308461	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35480231	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35664264	0.87[ASN][1000 genomes]
rs35867836	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs36118017	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4133253	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4679659	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4679660	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4679903	0.81[EUR][1000 genomes]
rs4679904	0.82[EUR][1000 genomes]
rs4679909	0.87[ASN][1000 genomes]
rs57718211	0.80[EUR][1000 genomes]
rs62272216	0.87[ASN][1000 genomes]
rs62272217	0.87[ASN][1000 genomes]
rs62272218	0.87[ASN][1000 genomes]
rs62272219	0.81[ASN][1000 genomes]
rs62272220	0.90[ASN][1000 genomes]
rs6763757	0.83[AMR][1000 genomes]
rs6763892	0.83[AMR][1000 genomes]
rs6773389	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6774379	0.87[ASN][1000 genomes]
rs6774566	0.87[ASN][1000 genomes]
rs6776873	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6777739	0.87[ASN][1000 genomes]
rs6779581	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6779671	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6787452	0.87[ASN][1000 genomes]
rs6788429	0.83[AMR][1000 genomes]
rs6797760	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6798462	0.87[ASN][1000 genomes]
rs6801373	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6803670	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806755	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7610939	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11927913	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160384000-160389200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:160385200-160395000	Weak transcription	Colonic Mucosa	Colon
3	chr3:160385400-160391200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:160385600-160388800	Weak transcription	NHLF	lung
5	chr3:160385600-160389000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:160385600-160389200	Weak transcription	Pancreas	Pancrea
7	chr3:160386200-160390000	Weak transcription	A549	lung
8	chr3:160386200-160393400	Weak transcription	Fetal Intestine Large	intestine
9	chr3:160386400-160388000	Weak transcription	GM12878-XiMat	blood
10	chr3:160386400-160388800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:160386400-160389000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:160386400-160391400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:160387800-160388800	Weak transcription	Stomach Mucosa	stomach
14	chr3:160387800-160389400	Enhancers	Small Intestine	intestine

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