Variant report

Variant	rs7750289
Chromosome Location	chr6:79902254-79902255
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:79901753..79904243-chr6:79911000..79912740,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10806164	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11752249	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs12191359	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12211094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13209338	0.82[GIH][hapmap]
rs13210296	0.91[GIH][hapmap]
rs13213305	0.82[GIH][hapmap]
rs2050436	1.00[EUR][1000 genomes]
rs28360567	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28360568	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34043789	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35711640	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4706085	0.91[CEU][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs4706757	0.93[EUR][1000 genomes]
rs66732383	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6930131	0.91[CEU][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs7766859	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9294132	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs9294133	0.82[CEU][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs9294134	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs9343882	1.00[EUR][1000 genomes]
rs9361502	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs9448657	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs989191	0.91[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];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
rs7750289	HMGN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79883000-79925000	Weak transcription	Pancreas	Pancrea
2	chr6:79898200-79908200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:79899000-79911600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:79899000-79912000	Weak transcription	Gastric	stomach
5	chr6:79899000-79912000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr6:79899000-79916800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:79899200-79924800	Weak transcription	Psoas Muscle	Psoas
8	chr6:79899400-79911600	Weak transcription	Fetal Intestine Large	intestine
9	chr6:79899400-79915600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:79899600-79910000	Weak transcription	Fetal Lung	lung
11	chr6:79899800-79924400	Weak transcription	Brain Anterior Caudate	brain
12	chr6:79900400-79911800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr6:79900800-79916000	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:79901000-79902400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
15	chr6:79901000-79911800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:79901200-79902400	ZNF genes & repeats	Aorta	Aorta
17	chr6:79901200-79927000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:79901400-79911000	Weak transcription	Adipose Nuclei	Adipose
19	chr6:79901400-79911800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:79901400-79911800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:79901400-79916000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:79901600-79902400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:79901600-79911800	Weak transcription	Spleen	Spleen
24	chr6:79901600-79912000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr6:79902000-79902400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:79902000-79902400	ZNF genes & repeats	Esophagus	oesophagus
27	chr6:79902000-79902400	ZNF genes & repeats	Dnd41	blood
28	chr6:79902200-79902400	ZNF genes & repeats	Primary B cells from cord blood	blood
29	chr6:79902200-79902400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
30	chr6:79902200-79902400	ZNF genes & repeats	Left Ventricle	heart
31	chr6:79902200-79902600	Strong transcription	Primary T cells from cord blood	blood
32	chr6:79902200-79902800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:79902200-79902800	Strong transcription	Stomach Smooth Muscle	stomach
34	chr6:79902200-79912200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:79902200-79917200	Weak transcription	Fetal Brain Male	brain

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