Variant report

Variant	rs11691302
Chromosome Location	chr2:48630784-48630785
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	chr2:48420748..48422643-chr2:48628237..48631229,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10182093	0.91[EUR][1000 genomes]
rs10191938	0.91[EUR][1000 genomes]
rs10195717	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10197359	0.90[EUR][1000 genomes]
rs11674217	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs11674317	0.80[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11674683	1.00[AFR][1000 genomes]
rs11675947	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11676078	0.83[EUR][1000 genomes]
rs11676925	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11677205	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11677350	1.00[AFR][1000 genomes]
rs11678825	0.84[EUR][1000 genomes]
rs11678934	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11679518	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11679685	0.91[EUR][1000 genomes]
rs11680968	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11682838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11683202	0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs11687276	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11687401	1.00[AFR][1000 genomes]
rs11687461	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11687771	0.82[CEU][hapmap]
rs11687851	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11688465	1.00[AFR][1000 genomes]
rs11689285	0.88[CEU][hapmap]
rs11690526	0.88[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs11691407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11692537	0.88[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs11694094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11694955	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13398456	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17325698	1.00[AFR][1000 genomes]
rs17397094	1.00[AFR][1000 genomes]
rs17397449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17397707	1.00[AFR][1000 genomes]
rs28505584	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2937	0.88[CEU][hapmap]
rs4364065	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6747738	0.88[CEU][hapmap]
rs72889641	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7573281	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7584796	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs952468	1.00[CEU][hapmap];1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription 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 target site	20 gene(s)	inside rSNPs	diseases
3	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv518718	chr2:48624007-48650308	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11691302	MSH6	cis	lymphoblastoid	seeQTL
rs11691302	CCDC128	Cis_1M	lymphoblastoid	RTeQTL
rs11691302	KLRAQ1	cis	parietal	SCAN
rs11691302	STON1-GTF2A1L	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48627400-48632200	Weak transcription	Fetal Intestine Large	intestine
2	chr2:48628200-48632200	Weak transcription	Fetal Intestine Small	intestine
3	chr2:48628200-48640000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:48628600-48633600	Weak transcription	Duodenum Mucosa	Duodenum

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