Variant report

Variant	rs35711640
Chromosome Location	chr6:79908483-79908484
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:79907861..79910027-chr6:79941828..79944247,2	K562	blood:

Variant related genes	Relation type
ENSG00000270362	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10806164	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11752249	0.95[EUR][1000 genomes]
rs12191359	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12211094	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2050436	1.00[EUR][1000 genomes]
rs28360567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28360568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34043789	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4706085	0.93[EUR][1000 genomes]
rs4706757	0.93[EUR][1000 genomes]
rs66732383	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6930131	0.93[EUR][1000 genomes]
rs7750289	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7766859	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9294132	0.93[EUR][1000 genomes]
rs9294133	0.93[EUR][1000 genomes]
rs9294134	0.93[EUR][1000 genomes]
rs9343882	1.00[EUR][1000 genomes]
rs9361502	0.92[EUR][1000 genomes]
rs9448657	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs989191	0.95[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
rs35711640	HMGN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79883000-79925000	Weak transcription	Pancreas	Pancrea
2	chr6:79899000-79911600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:79899000-79912000	Weak transcription	Gastric	stomach
4	chr6:79899000-79912000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:79899000-79916800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:79899200-79924800	Weak transcription	Psoas Muscle	Psoas
7	chr6:79899400-79911600	Weak transcription	Fetal Intestine Large	intestine
8	chr6:79899400-79915600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:79899600-79910000	Weak transcription	Fetal Lung	lung
10	chr6:79899800-79924400	Weak transcription	Brain Anterior Caudate	brain
11	chr6:79900400-79911800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:79900800-79916000	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:79901000-79911800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:79901200-79927000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:79901400-79911000	Weak transcription	Adipose Nuclei	Adipose
16	chr6:79901400-79911800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr6:79901400-79911800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:79901400-79916000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:79901600-79911800	Weak transcription	Spleen	Spleen
20	chr6:79901600-79912000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr6:79902200-79912200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:79902200-79917200	Weak transcription	Fetal Brain Male	brain
23	chr6:79902400-79909600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:79902400-79911000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr6:79902400-79911200	Weak transcription	Primary B cells from cord blood	blood
26	chr6:79902400-79911600	Weak transcription	Left Ventricle	heart
27	chr6:79902400-79911800	Weak transcription	Esophagus	oesophagus
28	chr6:79902400-79912000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:79902400-79919600	Weak transcription	Aorta	Aorta
30	chr6:79902600-79911800	Weak transcription	Primary T cells from cord blood	blood
31	chr6:79902800-79911000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:79902800-79911600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr6:79903200-79911600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr6:79903400-79911600	Weak transcription	HepG2	liver
35	chr6:79904200-79925000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:79904400-79912200	Weak transcription	Fetal Stomach	stomach
37	chr6:79905600-79908600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:79906000-79909800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:79906600-79911000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:79906600-79911800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr6:79906600-79911800	Weak transcription	Fetal Kidney	kidney
42	chr6:79906600-79911800	Weak transcription	Fetal Muscle Leg	muscle
43	chr6:79906600-79912000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr6:79906800-79910800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr6:79906800-79911800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:79906800-79935600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:79907000-79909800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:79907000-79911600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:79907000-79911600	Weak transcription	Liver	Liver
50	chr6:79907000-79911600	Weak transcription	GM12878-XiMat	blood

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