Variant report

Variant	rs9448657
Chromosome Location	chr6:79911290-79911291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:79901753..79904243-chr6:79911000..79912740,2	MCF-7	breast:
2	chr6:79910255..79912410-chr6:79943496..79945323,2	MCF-7	breast:
3	chr6:79903183..79905835-chr6:79909088..79912448,3	K562	blood:
4	chr6:79910795..79911579-chr6:80175671..80176696,3	MCF-7	breast:
5	chr6:79911023..79911795-chr6:80175584..80176322,2	MCF-7	breast:
6	chr6:79786696..79788317-chr6:79910357..79912297,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146247	Chromatin interaction
ENSG00000118418	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10806164	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11752249	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs12191359	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12211094	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13209338	0.82[GIH][hapmap]
rs13210296	0.91[GIH][hapmap]
rs13213305	0.82[GIH][hapmap]
rs2050436	0.97[EUR][1000 genomes]
rs28360567	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28360568	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34043789	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35711640	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4706085	0.91[CEU][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.96[EUR][1000 genomes]
rs4706757	0.96[EUR][1000 genomes]
rs66732383	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6930131	0.91[CEU][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.96[EUR][1000 genomes]
rs7750289	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7766859	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9294132	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs9294133	0.82[CEU][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.96[EUR][1000 genomes]
rs9294134	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs9343882	0.97[EUR][1000 genomes]
rs9361502	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs989191	0.91[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.97[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
rs9448657	HMGN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79883000-79925000	Weak transcription	Pancreas	Pancrea
2	chr6:79899000-79911600	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	chr6:79899800-79924400	Weak transcription	Brain Anterior Caudate	brain
10	chr6:79900400-79911800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:79900800-79916000	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:79901000-79911800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:79901200-79927000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:79901400-79911800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:79901400-79911800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:79901400-79916000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:79901600-79911800	Weak transcription	Spleen	Spleen
18	chr6:79901600-79912000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:79902200-79912200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:79902200-79917200	Weak transcription	Fetal Brain Male	brain
21	chr6:79902400-79911600	Weak transcription	Left Ventricle	heart
22	chr6:79902400-79911800	Weak transcription	Esophagus	oesophagus
23	chr6:79902400-79912000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:79902400-79919600	Weak transcription	Aorta	Aorta
25	chr6:79902600-79911800	Weak transcription	Primary T cells from cord blood	blood
26	chr6:79902800-79911600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr6:79903200-79911600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:79903400-79911600	Weak transcription	HepG2	liver
29	chr6:79904200-79925000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:79904400-79912200	Weak transcription	Fetal Stomach	stomach
31	chr6:79906600-79911800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr6:79906600-79911800	Weak transcription	Fetal Kidney	kidney
33	chr6:79906600-79911800	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:79906600-79912000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:79906800-79911800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:79906800-79935600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:79907000-79911600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:79907000-79911600	Weak transcription	Liver	Liver
39	chr6:79907000-79911600	Weak transcription	GM12878-XiMat	blood
40	chr6:79907000-79924800	Weak transcription	NH-A	brain
41	chr6:79907200-79916000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:79907200-79926000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:79907400-79911600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:79907400-79911800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:79907400-79916000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr6:79907400-79942800	Weak transcription	HSMM	muscle
47	chr6:79907600-79911600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr6:79907600-79924400	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:79907600-79940800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr6:79907800-79911600	Weak transcription	Primary monocytes fromperipheralblood	blood

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