Variant report

Variant	rs13200164
Chromosome Location	chr6:79939422-79939423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:79938105..79940918-chr6:79942151..79944715,2	K562	blood:
2	chr6:79936163..79939514-chr6:79941809..79945122,5	MCF-7	breast:
3	chr6:79786645..79789143-chr6:79938512..79942027,3	MCF-7	breast:
4	chr6:79934006..79937126-chr6:79938281..79940748,3	K562	blood:

Variant related genes	Relation type
ENSG00000118418	Chromatin interaction
ENSG00000146247	Chromatin interaction
ENSG00000270362	Chromatin interaction

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

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

rs_ID	r²[population]
rs13203405	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13203510	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13209338	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13209772	1.00[EUR][1000 genomes]
rs13210296	1.00[EUR][1000 genomes]
rs13210935	1.00[EUR][1000 genomes]
rs13212378	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13213305	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13217071	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13217706	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13220697	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28360569	1.00[EUR][1000 genomes]
rs34057607	0.98[EUR][1000 genomes]
rs34493475	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34688736	0.91[EUR][1000 genomes]
rs35099838	0.94[EUR][1000 genomes]
rs35201024	1.00[EUR][1000 genomes]
rs35233121	1.00[EUR][1000 genomes]
rs35237040	0.91[EUR][1000 genomes]
rs35332837	1.00[EUR][1000 genomes]
rs35742788	1.00[EUR][1000 genomes]
rs35838792	0.87[EUR][1000 genomes]
rs36116051	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55773960	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66513375	1.00[EUR][1000 genomes]
rs66633427	1.00[EUR][1000 genomes]
rs66809524	1.00[EUR][1000 genomes]
rs66869917	1.00[EUR][1000 genomes]
rs72893783	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];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
rs13200164	HMGN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79907400-79942800	Weak transcription	HSMM	muscle
2	chr6:79907600-79940800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr6:79912400-79940600	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr6:79912800-79942600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:79913200-79943000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:79913200-79943200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:79916400-79943200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:79917800-79941000	Weak transcription	Hela-S3	cervix
9	chr6:79918200-79942000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:79920400-79940600	Weak transcription	Dnd41	blood
11	chr6:79920400-79943000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:79925200-79939600	Weak transcription	Fetal Brain Male	brain
13	chr6:79925400-79939600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:79925400-79940000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr6:79925400-79940600	Weak transcription	Placenta	Placenta
16	chr6:79925400-79942600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:79925800-79940600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:79925800-79941800	Weak transcription	Brain Angular Gyrus	brain
19	chr6:79925800-79942000	Weak transcription	Adipose Nuclei	Adipose
20	chr6:79925800-79942000	Weak transcription	Brain Anterior Caudate	brain
21	chr6:79925800-79942800	Weak transcription	Liver	Liver
22	chr6:79926600-79942000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:79927200-79939800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:79927400-79942600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr6:79927600-79940800	Weak transcription	Brain Hippocampus Middle	brain
26	chr6:79927800-79940800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:79927800-79942000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr6:79927800-79942800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:79927800-79942800	Weak transcription	Primary T cells from cord blood	blood
30	chr6:79928000-79942000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:79929000-79942000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr6:79929000-79942000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:79929200-79941600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:79929600-79941400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr6:79929800-79941000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:79930200-79941800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:79931200-79942800	Weak transcription	Left Ventricle	heart
38	chr6:79931600-79940600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr6:79931600-79942000	Weak transcription	Gastric	stomach
40	chr6:79932400-79942400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:79933800-79942600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:79934200-79942200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr6:79934200-79942400	Weak transcription	Primary B cells from cord blood	blood
44	chr6:79934600-79940600	Weak transcription	Fetal Lung	lung
45	chr6:79934600-79941600	Weak transcription	Fetal Intestine Small	intestine
46	chr6:79935800-79941600	Weak transcription	Colon Smooth Muscle	Colon
47	chr6:79935800-79942000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr6:79936000-79942000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr6:79936200-79939800	Weak transcription	NHEK	skin
50	chr6:79936200-79940800	Weak transcription	Right Ventricle	heart

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