Variant report

Variant	rs10514713
Chromosome Location	chr3:46543617-46543618
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46542684..46544753-chr3:46554640..46556935,2	K562	blood:
2	chr3:46539462..46541927-chr3:46542900..46546171,3	K562	blood:
3	chr3:46542254..46545139-chr3:46598522..46600340,2	K562	blood:
4	chr3:46539335..46541927-chr3:46542072..46545650,5	K562	blood:

Variant related genes	Relation type
ENSG00000268324	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10865941	0.96[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs11130093	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130094	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11705987	1.00[YRI][hapmap]
rs11706090	0.84[EUR][1000 genomes]
rs11714743	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11719033	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12489007	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12489117	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490169	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12496623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496864	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629867	1.00[YRI][hapmap]
rs12637386	1.00[YRI][hapmap]
rs12638228	0.84[EUR][1000 genomes]
rs1402151	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1520483	0.84[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs17030627	0.86[ASW][hapmap];0.81[CHD][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];1.00[YRI][hapmap]
rs2037391	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2068099	1.00[YRI][hapmap]
rs2139634	0.85[EUR][1000 genomes]
rs2280407	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28413725	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3934896	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55950019	0.83[EUR][1000 genomes]
rs56233078	0.83[EUR][1000 genomes]
rs60986461	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6762703	0.84[EUR][1000 genomes]
rs6763280	0.85[EUR][1000 genomes]
rs883739	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs885485	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs885486	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014624	chr3:46463424-46549188	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1009892	chr3:46496775-46546918	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv536553	chr3:46496775-46546918	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10514713	LRRC2	cis	parietal	SCAN
rs10514713	KIF9	cis	cerebellum	SCAN
rs10514713	LRRC2	cis	brain	seeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46533000-46544200	Weak transcription	Psoas Muscle	Psoas
2	chr3:46537200-46546200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:46537200-46547000	Enhancers	Fetal Thymus	thymus
4	chr3:46537200-46550200	Enhancers	K562	blood
5	chr3:46538200-46546800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:46538600-46544600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:46538800-46543800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:46538800-46544400	Weak transcription	Right Atrium	heart
9	chr3:46538800-46546600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:46538800-46546800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:46539000-46547200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:46539200-46547600	Weak transcription	Spleen	Spleen
13	chr3:46539800-46545400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr3:46540000-46544200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:46540800-46543800	Enhancers	Primary T cells from cord blood	blood
16	chr3:46541000-46557600	Weak transcription	Left Ventricle	heart
17	chr3:46541000-46580200	Weak transcription	Fetal Heart	heart
18	chr3:46541200-46562200	Weak transcription	Right Ventricle	heart
19	chr3:46541600-46543800	Enhancers	NH-A	brain
20	chr3:46541600-46545200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:46541600-46545600	Enhancers	Fetal Muscle Leg	muscle
22	chr3:46541600-46545600	Enhancers	HSMM	muscle
23	chr3:46542000-46544000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr3:46542000-46545200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:46542000-46545600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:46542000-46547000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:46542200-46544600	Weak transcription	NHLF	lung
28	chr3:46542200-46545200	Enhancers	Primary hematopoietic stem cells	blood
29	chr3:46542200-46545600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr3:46542200-46545800	Enhancers	HSMMtube	muscle
31	chr3:46542800-46544400	Weak transcription	Dnd41	blood
32	chr3:46543000-46544800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:46543200-46544400	Enhancers	GM12878-XiMat	blood
34	chr3:46543200-46544600	Weak transcription	Thymus	Thymus
35	chr3:46543200-46545000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:46543400-46544400	Weak transcription	Placenta	Placenta
37	chr3:46543400-46545000	Enhancers	Liver	Liver
38	chr3:46543400-46547400	Weak transcription	Primary B cells from cord blood	blood
39	chr3:46543600-46544000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:46543600-46544800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr3:46543600-46544800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:46543600-46545000	Weak transcription	NHDF-Ad	bronchial
43	chr3:46543600-46545200	Weak transcription	Osteobl	bone

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