Variant report

Variant	rs10485304
Chromosome Location	chr6:85824323-85824324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 5 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2104467	1.00[YRI][hapmap]
rs867744	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv520873	chr6:85824323-85834204	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10485304	RPS4Y1	trans	lymphoblastoid	seeQTL
rs10485304	CYB5R4	cis	cerebellum	SCAN
rs10485304	USP9Y	trans	lymphoblastoid	seeQTL
rs10485304	NT5E	cis	cerebellum	SCAN
rs10485304	EIF1AX	trans	lymphoblastoid	seeQTL
rs10485304	KDM6A	trans	lymphoblastoid	seeQTL
rs10485304	DDX3Y	trans	lymphoblastoid	seeQTL
rs10485304	HDHD1	trans	lymphoblastoid	seeQTL
rs10485304	XIST	trans	lymphoblastoid	seeQTL
rs10485304	KDM5D	trans	lymphoblastoid	seeQTL
rs10485304	EIF1AY	trans	lymphoblastoid	seeQTL
rs10485304	UTY	trans	lymphoblastoid	seeQTL
rs10485304	ZRSR2	trans	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:85822800-85825400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr6:85823400-85824400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:85823400-85824400	Active TSS	Psoas Muscle	Psoas
4	chr6:85823400-85824600	Flanking Active TSS	Osteobl	bone
5	chr6:85823800-85824400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:85823800-85824400	Weak transcription	Fetal Stomach	stomach
7	chr6:85823800-85824400	Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr6:85823800-85824400	Active TSS	Stomach Smooth Muscle	stomach
9	chr6:85823800-85824600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr6:85823800-85824600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:85823800-85824600	Flanking Active TSS	Fetal Brain Female	brain
12	chr6:85823800-85824600	Active TSS	Right Atrium	heart
13	chr6:85824000-85824400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr6:85824000-85824400	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr6:85824000-85824400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:85824000-85824400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:85824000-85824400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:85824000-85824400	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr6:85824000-85824400	Enhancers	Aorta	Aorta
20	chr6:85824000-85824400	Active TSS	Brain Cingulate Gyrus	brain
21	chr6:85824000-85824400	Active TSS	Brain Hippocampus Middle	brain
22	chr6:85824000-85824400	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
23	chr6:85824000-85824400	Active TSS	Fetal Kidney	kidney
24	chr6:85824000-85824400	Flanking Active TSS	Fetal Lung	lung
25	chr6:85824000-85824400	Active TSS	Fetal Muscle Trunk	muscle
26	chr6:85824000-85824400	Active TSS	Rectal Smooth Muscle	rectum
27	chr6:85824000-85824400	Flanking Active TSS	HMEC	breast
28	chr6:85824000-85824600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:85824000-85824600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:85824000-85824600	Active TSS	Colon Smooth Muscle	Colon
31	chr6:85824200-85824400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:85824200-85824400	Active TSS	Brain Anterior Caudate	brain
33	chr6:85824200-85824400	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr6:85824200-85824400	Active TSS	Fetal Muscle Leg	muscle
35	chr6:85824200-85824400	Active TSS	Ovary	ovary
36	chr6:85824200-85824400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr6:85824200-85824400	Flanking Bivalent TSS/Enh	HSMMtube	muscle
38	chr6:85824200-85824400	Flanking Active TSS	NHDF-Ad	bronchial
39	chr6:85824200-85824400	Flanking Active TSS	NHLF	lung
40	chr6:85824200-85824600	Bivalent/Poised TSS	Fetal Brain Male	brain

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