Variant report

Variant	rs35237040
Chromosome Location	chr6:79899616-79899617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13200164	0.91[EUR][1000 genomes]
rs13203405	0.91[EUR][1000 genomes]
rs13203510	0.91[EUR][1000 genomes]
rs13209338	0.91[EUR][1000 genomes]
rs13209772	0.91[EUR][1000 genomes]
rs13210296	0.91[EUR][1000 genomes]
rs13210935	0.91[EUR][1000 genomes]
rs13212378	0.91[EUR][1000 genomes]
rs13213305	0.91[EUR][1000 genomes]
rs13217071	0.91[EUR][1000 genomes]
rs13217706	0.91[EUR][1000 genomes]
rs13220697	0.94[EUR][1000 genomes]
rs28360569	0.91[EUR][1000 genomes]
rs34057607	0.94[EUR][1000 genomes]
rs34493475	0.91[EUR][1000 genomes]
rs34688736	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35099838	0.86[EUR][1000 genomes]
rs35201024	0.91[EUR][1000 genomes]
rs35233121	0.91[EUR][1000 genomes]
rs35332837	0.91[EUR][1000 genomes]
rs35742788	0.91[EUR][1000 genomes]
rs35838792	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36116051	0.94[EUR][1000 genomes]
rs55773960	0.94[EUR][1000 genomes]
rs66513375	0.91[EUR][1000 genomes]
rs66633427	0.91[EUR][1000 genomes]
rs66809524	0.91[EUR][1000 genomes]
rs66869917	0.91[EUR][1000 genomes]
rs72893783	0.91[EUR][1000 genomes]
rs9448670	0.85[EUR][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	nsv830706	chr6:79825910-79994878	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35237040	HMGN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79883000-79925000	Weak transcription	Pancreas	Pancrea
2	chr6:79890800-79902000	Weak transcription	Esophagus	oesophagus
3	chr6:79892800-79900800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:79893000-79902200	Weak transcription	Left Ventricle	heart
5	chr6:79895000-79901200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:79896800-79899800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:79898000-79900400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:79898200-79899800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:79898200-79908200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:79898400-79900000	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr6:79898800-79899800	Enhancers	Brain Anterior Caudate	brain
12	chr6:79898800-79900600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr6:79899000-79900400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:79899000-79901200	Weak transcription	Aorta	Aorta
15	chr6:79899000-79911600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr6:79899000-79912000	Weak transcription	Gastric	stomach
17	chr6:79899000-79912000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:79899000-79916800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:79899200-79924800	Weak transcription	Psoas Muscle	Psoas
20	chr6:79899400-79901000	Weak transcription	Adipose Nuclei	Adipose
21	chr6:79899400-79901000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:79899400-79901200	Weak transcription	Fetal Brain Male	brain
23	chr6:79899400-79911600	Weak transcription	Fetal Intestine Large	intestine
24	chr6:79899400-79915600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:79899600-79910000	Weak transcription	Fetal Lung	lung

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