Variant report

Variant	rs6492262
Chromosome Location	chr13:111000752-111000753
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:111000060..111002459-chr13:111005280..111006914,2	MCF-7	breast:
2	chr13:110998747..111001363-chr13:111017534..111020102,2	MCF-7	breast:
3	chr13:110975551..110977167-chr13:110999364..111001106,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1041317	0.93[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4771668	0.85[YRI][hapmap]
rs4771670	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773158	0.87[EUR][1000 genomes]
rs4773160	1.00[MEX][hapmap]
rs4773161	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4773164	0.88[YRI][hapmap]
rs9583487	1.00[MEX][hapmap]
rs9588143	1.00[MEX][hapmap]

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	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1049454	chr13:110950768-111006547	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6492262	DDX6	trans	brain	seeQTL
rs6492262	RFPL2	trans	brain	seeQTL
rs6492262	SLC5A3	trans	brain	seeQTL
rs6492262	GBP4	trans	brain	seeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:110972600-111007200	Weak transcription	Gastric	stomach
2	chr13:110980200-111002800	Weak transcription	Fetal Brain Male	brain
3	chr13:110992000-111001600	Weak transcription	Brain Substantia Nigra	brain
4	chr13:110993800-111007200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:110994000-111004400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr13:110994000-111019600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr13:110994400-111002800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr13:110994400-111007200	Weak transcription	Fetal Kidney	kidney
9	chr13:110995200-111005200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr13:110995200-111007000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr13:110995400-111004200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr13:110995600-111005800	Weak transcription	Fetal Lung	lung
13	chr13:110996000-111009800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr13:110997000-111001000	Enhancers	Left Ventricle	heart
15	chr13:110997800-111002800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:110998000-111000800	Enhancers	Spleen	Spleen
17	chr13:110998000-111001800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:110998000-111002200	Enhancers	Right Ventricle	heart
19	chr13:110998000-111002800	Enhancers	Fetal Heart	heart
20	chr13:110998200-111000800	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr13:110998400-111000800	Enhancers	Placenta	Placenta
22	chr13:110998400-111000800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
23	chr13:110998600-111001000	Enhancers	NHLF	lung
24	chr13:110998600-111003000	Enhancers	Colon Smooth Muscle	Colon
25	chr13:110998800-111001200	Enhancers	NHDF-Ad	bronchial
26	chr13:110999000-111000800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr13:110999000-111002200	Enhancers	Adipose Nuclei	Adipose
28	chr13:110999000-111002800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr13:110999200-111001800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr13:110999200-111003600	Enhancers	Right Atrium	heart
31	chr13:110999400-111000800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr13:110999400-111000800	Flanking Active TSS	NHEK	skin
33	chr13:110999600-111000800	Flanking Active TSS	Osteobl	bone
34	chr13:110999800-111000800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr13:110999800-111000800	Flanking Active TSS	Hela-S3	cervix
36	chr13:110999800-111001000	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr13:110999800-111001200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr13:110999800-111001200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr13:110999800-111001200	Enhancers	Rectal Smooth Muscle	rectum
40	chr13:110999800-111004400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr13:110999800-111005000	Weak transcription	Fetal Intestine Large	intestine
42	chr13:111000000-111001000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr13:111000000-111001200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr13:111000000-111001600	Weak transcription	Fetal Stomach	stomach
45	chr13:111000000-111009400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr13:111000000-111009800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr13:111000200-111001600	Weak transcription	Psoas Muscle	Psoas
48	chr13:111000200-111005800	Weak transcription	Fetal Intestine Small	intestine
49	chr13:111000400-111000800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr13:111000400-111000800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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