Variant report

Variant	rs13210296
Chromosome Location	chr6:79922256-79922257
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:79922096..79924489-chr6:79928328..79930333,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs13200164	1.00[EUR][1000 genomes]
rs13203405	0.82[CEU][hapmap];1.00[EUR][1000 genomes]
rs13203510	0.82[CEU][hapmap];1.00[EUR][1000 genomes]
rs13209338	0.82[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs13209772	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13210935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13212378	1.00[EUR][1000 genomes]
rs13213305	0.82[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs13217071	0.82[CEU][hapmap];1.00[EUR][1000 genomes]
rs13217706	1.00[EUR][1000 genomes]
rs13220697	0.82[CEU][hapmap];0.98[EUR][1000 genomes]
rs28360569	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34057607	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34493475	1.00[EUR][1000 genomes]
rs34688736	0.91[EUR][1000 genomes]
rs35099838	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35201024	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35233121	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35237040	0.91[EUR][1000 genomes]
rs35332837	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35742788	0.95[AFR][1000 genomes];1.00[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	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66633427	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66809524	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66869917	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72893783	1.00[EUR][1000 genomes]
rs9448657	0.91[GIH][hapmap]
rs9448670	0.90[EUR][1000 genomes]
rs989191	0.91[GIH][hapmap]

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
rs13210296	HMGN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79883000-79925000	Weak transcription	Pancreas	Pancrea
2	chr6:79899200-79924800	Weak transcription	Psoas Muscle	Psoas
3	chr6:79899800-79924400	Weak transcription	Brain Anterior Caudate	brain
4	chr6:79901200-79927000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:79904200-79925000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:79906800-79935600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:79907000-79924800	Weak transcription	NH-A	brain
8	chr6:79907200-79926000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:79907400-79942800	Weak transcription	HSMM	muscle
10	chr6:79907600-79924400	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:79907600-79940800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr6:79908400-79924800	Weak transcription	Fetal Heart	heart
13	chr6:79908400-79938600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:79910200-79924400	Weak transcription	Brain Angular Gyrus	brain
15	chr6:79910200-79925000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:79910800-79924600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:79910800-79935600	Weak transcription	NHEK	skin
18	chr6:79911000-79928800	Weak transcription	Brain Substantia Nigra	brain
19	chr6:79912200-79924800	Weak transcription	Small Intestine	intestine
20	chr6:79912400-79940600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr6:79912600-79925000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr6:79912600-79927600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:79912600-79931000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:79912800-79924800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:79912800-79926600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:79912800-79942600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr6:79913200-79926400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr6:79913200-79943000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:79913200-79943200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:79913800-79924800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:79914000-79924800	Weak transcription	HepG2	liver
32	chr6:79914200-79923800	Weak transcription	Fetal Brain Female	brain
33	chr6:79916400-79925200	Weak transcription	HMEC	breast
34	chr6:79916400-79930400	Weak transcription	Brain Germinal Matrix	brain
35	chr6:79916400-79935400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:79916400-79943200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:79916600-79925000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:79916600-79925200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:79916600-79927600	Weak transcription	Esophagus	oesophagus
40	chr6:79916600-79933000	Weak transcription	Spleen	Spleen
41	chr6:79916800-79924800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:79916800-79925000	Weak transcription	Lung	lung
43	chr6:79916800-79927600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr6:79917400-79924400	Weak transcription	Fetal Intestine Small	intestine
45	chr6:79917600-79924800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr6:79917800-79924800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:79917800-79924800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr6:79917800-79929200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:79917800-79929600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:79917800-79941000	Weak transcription	Hela-S3	cervix

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