Variant report

Variant	rs607349
Chromosome Location	chr11:93513530-93513531
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000210825	Chromatin interaction
ENSG00000221170	Chromatin interaction
ENSG00000207145	Chromatin interaction
ENSG00000239195	Chromatin interaction
ENSG00000207112	Chromatin interaction
ENSG00000206799	Chromatin interaction
ENSG00000166012	Chromatin interaction
ENSG00000042429	Chromatin interaction
ENSG00000182919	Chromatin interaction
ENSG00000207304	Chromatin interaction
ENSG00000206834	Chromatin interaction
ENSG00000202314	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10831103	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10831104	1.00[JPT][hapmap]
rs11020511	0.89[EUR][1000 genomes]
rs11020515	0.83[EUR][1000 genomes]
rs11603339	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11603364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17650369	0.87[CHD][hapmap]
rs2895508	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3097323	0.85[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap]
rs596052	0.98[EUR][1000 genomes]
rs613610	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621801	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs635963	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs643261	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs644306	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.88[ASN][1000 genomes]
rs668546	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs677867	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs685865	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7310	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[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	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv898182	chr11:93381845-93637462	Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv832232	chr11:93401314-93549438	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs607349	MED17	cis	parietal	SCAN
rs607349	MED17	cis	cerebellum	SCAN
rs607349	SCARNA9	cis	parietal	SCAN
rs607349	C11orf54	cis	Artery Aorta	GTEx
rs607349	C11orf54	cis	cerebellum	SCAN
rs607349	MED17	Cis_1M	lymphoblastoid	RTeQTL
rs607349	C11orf54	cis	Esophagus Muscularis	GTEx
rs607349	C11orf54	cis	parietal	SCAN
rs607349	FUT4	cis	cerebellum	SCAN
rs607349	ENDOD1	cis	cerebellum	SCAN
rs607349	C11orf54	cis	Esophagus Mucosa	GTEx
rs607349	GPR83	cis	cerebellum	SCAN
rs607349	C11orf54	cis	Artery Tibial	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93492200-93516600	Weak transcription	Psoas Muscle	Psoas
2	chr11:93492200-93516800	Weak transcription	Right Ventricle	heart
3	chr11:93496000-93513600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:93498000-93516600	Weak transcription	Brain Hippocampus Middle	brain
5	chr11:93498600-93516600	Weak transcription	Hela-S3	cervix
6	chr11:93499200-93516600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr11:93499800-93516600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr11:93505800-93516600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:93506200-93516600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:93506400-93516600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr11:93506600-93516600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:93506600-93516600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:93506800-93516600	Weak transcription	Brain Germinal Matrix	brain
14	chr11:93507600-93516600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:93510400-93516400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:93512000-93516600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:93513000-93513800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
18	chr11:93513200-93513600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:93513400-93516600	Weak transcription	Fetal Muscle Trunk	muscle

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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