Variant report

Variant	rs35233121
Chromosome Location	chr6:79926989-79926990
allele	G/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	1.00[EUR][1000 genomes]
rs13203405	1.00[EUR][1000 genomes]
rs13203510	1.00[EUR][1000 genomes]
rs13209338	1.00[EUR][1000 genomes]
rs13209772	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13210296	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13210935	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13212378	1.00[EUR][1000 genomes]
rs13213305	1.00[EUR][1000 genomes]
rs13217071	1.00[EUR][1000 genomes]
rs13217706	1.00[EUR][1000 genomes]
rs13220697	0.98[EUR][1000 genomes]
rs28360569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34057607	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34493475	1.00[EUR][1000 genomes]
rs34688736	0.91[EUR][1000 genomes]
rs35099838	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35201024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35237040	0.91[EUR][1000 genomes]
rs35332837	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35742788	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35838792	0.87[EUR][1000 genomes]
rs36116051	0.98[EUR][1000 genomes]
rs55773960	0.98[EUR][1000 genomes]
rs66513375	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66633427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66809524	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66869917	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72893783	1.00[EUR][1000 genomes]
rs9448670	0.90[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
rs35233121	HMGN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79901200-79927000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:79906800-79935600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:79907400-79942800	Weak transcription	HSMM	muscle
4	chr6:79907600-79940800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr6:79908400-79938600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:79910800-79935600	Weak transcription	NHEK	skin
7	chr6:79911000-79928800	Weak transcription	Brain Substantia Nigra	brain
8	chr6:79912400-79940600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr6:79912600-79927600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:79912600-79931000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:79912800-79942600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:79913200-79943000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:79913200-79943200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:79916400-79930400	Weak transcription	Brain Germinal Matrix	brain
15	chr6:79916400-79935400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:79916400-79943200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:79916600-79927600	Weak transcription	Esophagus	oesophagus
18	chr6:79916600-79933000	Weak transcription	Spleen	Spleen
19	chr6:79916800-79927600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:79917800-79929200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:79917800-79929600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:79917800-79941000	Weak transcription	Hela-S3	cervix
23	chr6:79918200-79942000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr6:79920200-79927400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:79920200-79928800	Weak transcription	GM12878-XiMat	blood
26	chr6:79920200-79933400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr6:79920400-79927000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr6:79920400-79927000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:79920400-79927400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:79920400-79927400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:79920400-79940600	Weak transcription	Dnd41	blood
32	chr6:79920400-79943000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr6:79920600-79927600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:79920600-79927600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:79920600-79928600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:79920600-79931400	Weak transcription	Aorta	Aorta
37	chr6:79920800-79939200	Weak transcription	Fetal Thymus	thymus
38	chr6:79921600-79933000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:79924800-79927800	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr6:79924800-79928800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr6:79924800-79929800	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr6:79925000-79933600	Weak transcription	Primary B cells from cord blood	blood
43	chr6:79925000-79935400	Weak transcription	Fetal Kidney	kidney
44	chr6:79925200-79928200	Weak transcription	NH-A	brain
45	chr6:79925200-79939600	Weak transcription	Fetal Brain Male	brain
46	chr6:79925400-79927200	Weak transcription	Brain Hippocampus Middle	brain
47	chr6:79925400-79927600	Weak transcription	Lung	lung
48	chr6:79925400-79927600	Weak transcription	Ovary	ovary
49	chr6:79925400-79931000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr6:79925400-79931000	Weak transcription	Left Ventricle	heart

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