Variant report

Variant	rs2613946
Chromosome Location	chr3:112825573-112825574
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11923603	0.81[CHD][hapmap]
rs1461107	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1795168	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1795170	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1797623	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1797624	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1797625	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1797626	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2245698	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2613948	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2613961	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2700198	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2700200	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2700201	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2700227	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2926813	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs871596	0.81[ASN][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv877344	chr3:112789865-112854339	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2613946	RP11-572M11.3	cis	Nerve Tibial	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112808800-112832400	Weak transcription	Primary T cells from cord blood	blood
2	chr3:112819400-112830400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:112821200-112825800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:112821600-112825800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr3:112821800-112825600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr3:112822000-112826400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:112822200-112825800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:112822200-112826200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:112822200-112829400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:112822400-112825800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr3:112823000-112825600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr3:112823000-112825800	Enhancers	Fetal Stomach	stomach
13	chr3:112823200-112826600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:112823400-112827600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:112823400-112827600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:112824000-112825800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr3:112824200-112825800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr3:112824200-112828000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:112824200-112828800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:112824200-112829800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:112824400-112828000	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:112824400-112829400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:112824600-112825600	Enhancers	H9 Cell Line	embryonic stem cell
24	chr3:112824600-112825800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:112824600-112826000	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr3:112824600-112829200	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:112824800-112825600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:112825000-112828000	Weak transcription	Ovary	ovary
29	chr3:112825000-112829200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:112825000-112829600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:112825000-112829800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:112825200-112829800	Weak transcription	Placenta Amnion	Placenta Amnion

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