Variant report

Variant	rs3210683
Chromosome Location	chr15:75890612-75890613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75890174..75890978-chr15:75976106..75976698,2	MCF-7	breast:
2	chr15:75887095..75893245-chr15:75929965..75934746,7	MCF-7	breast:
3	chr15:75871001..75873380-chr15:75889337..75891497,2	K562	blood:
4	chr15:75870299..75873380-chr15:75889337..75893245,3	K562	blood:
5	chr15:75889690..75891228-chr15:75901525..75903473,2	MCF-7	breast:
6	chr15:75871281..75872816-chr15:75889929..75891455,2	MCF-7	breast:
7	chr15:75889918..75890742-chr15:75975684..75976291,2	K562	blood:

Variant related genes	Relation type
ENSG00000169410	Chromatin interaction
ENSG00000177971	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1128585	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28372916	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28372917	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886453	0.82[EUR][1000 genomes]
rs4886723	0.87[EUR][1000 genomes]
rs55737327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56178382	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56267307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73436854	0.88[EUR][1000 genomes]
rs8025681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs8027749	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8041160	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv530345	chr15:75628556-75951011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
6	nsv482802	chr15:75686519-75899896	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
8	nsv531902	chr15:75724505-75919237	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3210683	CTD-2323K18.1	cis	Thyroid	GTEx
rs3210683	CTD-2323K18.1	cis	lung	GTEx
rs3210683	SNUPN	cis	Thyroid	GTEx
rs3210683	MAN2C1	cis	Whole Blood	GTEx
rs3210683	NEIL1	cis	cerebellum	SCAN
rs3210683	MAN2C1	cis	Esophagus Muscularis	GTEx
rs3210683	SGK269	cis	parietal	SCAN
rs3210683	MAN2C1	cis	parietal	SCAN
rs3210683	SNUPN	cis	parietal	SCAN
rs3210683	SEMA7A	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75872400-75891600	Weak transcription	Pancreas	Pancrea
2	chr15:75872400-75892000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:75872400-75898600	Weak transcription	Small Intestine	intestine
4	chr15:75876800-75899200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:75877600-75901800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:75880400-75912400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:75882200-75910400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:75882800-75911400	Strong transcription	Fetal Muscle Leg	muscle
9	chr15:75883400-75911800	Strong transcription	Fetal Stomach	stomach
10	chr15:75883600-75901000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr15:75883800-75903600	Strong transcription	Stomach Smooth Muscle	stomach
12	chr15:75883800-75911600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:75883800-75911800	Strong transcription	Fetal Muscle Trunk	muscle
14	chr15:75884000-75893600	Strong transcription	Spleen	Spleen
15	chr15:75884200-75893800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr15:75884200-75894400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:75884800-75898600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:75886000-75890800	Strong transcription	Placenta	Placenta
19	chr15:75886000-75891000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:75886000-75893600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:75886000-75895200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:75886000-75895600	Strong transcription	Fetal Brain Female	brain
23	chr15:75886000-75896400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:75886000-75898000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:75886000-75898200	Strong transcription	Fetal Thymus	thymus
26	chr15:75886000-75912400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:75886200-75893800	Strong transcription	Primary B cells from peripheral blood	blood
28	chr15:75886200-75903200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr15:75886400-75893400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:75886400-75905400	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:75886600-75890800	Strong transcription	HSMMtube	muscle
32	chr15:75886600-75891400	Strong transcription	Placenta Amnion	Placenta Amnion
33	chr15:75886600-75894400	Strong transcription	Primary B cells from cord blood	blood
34	chr15:75886600-75894400	Strong transcription	HSMM	muscle
35	chr15:75886600-75895600	Strong transcription	Thymus	Thymus
36	chr15:75886600-75897800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:75886600-75903400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:75886800-75891000	Strong transcription	Hela-S3	cervix
39	chr15:75886800-75893400	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr15:75886800-75893600	Strong transcription	Fetal Lung	lung
41	chr15:75886800-75893600	Strong transcription	A549	lung
42	chr15:75886800-75893800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:75886800-75893800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:75886800-75894200	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr15:75886800-75894400	Strong transcription	Osteobl	bone
46	chr15:75886800-75895400	Strong transcription	Ovary	ovary
47	chr15:75887600-75893800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr15:75887600-75893800	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr15:75887600-75894000	Strong transcription	Fetal Intestine Large	intestine
50	chr15:75887600-75912400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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