Variant report

Variant	rs247963
Chromosome Location	chr5:99931937-99931938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs13876	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs154706	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154710	0.82[ASN][1000 genomes]
rs154711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs154712	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs173552	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173553	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs174041	0.97[ASN][1000 genomes]
rs1840984	0.97[ASN][1000 genomes]
rs184888	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs190326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2370612	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs247933	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs247934	0.81[ASN][1000 genomes]
rs247936	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap]
rs247939	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.81[ASN][1000 genomes]
rs247944	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs247956	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247957	1.00[ASN][1000 genomes]
rs247958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247959	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs247960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247962	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs247964	1.00[ASN][1000 genomes]
rs258540	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs258541	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs258544	0.97[ASN][1000 genomes]
rs258545	0.97[ASN][1000 genomes]
rs258546	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26028	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs26030	1.00[CEU][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs26031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[ASN][1000 genomes]
rs26032	0.81[ASN][1000 genomes]
rs26034	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs27458	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs27626	1.00[CEU][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs32236	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[ASN][1000 genomes]
rs32237	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs32260	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs32261	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap]
rs573843	1.00[CEU][hapmap]
rs6870025	1.00[CEU][hapmap];0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599165	chr5:99469004-100063039	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv948969	chr5:99534096-100133827	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
4	nsv882462	chr5:99745767-100060150	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1025890	chr5:99745775-99936186	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1017420	chr5:99745775-100133140	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv537825	chr5:99745775-100133140	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv1018395	chr5:99827242-100003207	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv823158	chr5:99912491-99960408	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs247963	MLX	trans	parietal	SCAN
rs247963	FAM174A	cis	parietal	SCAN
rs247963	LIX1	cis	parietal	SCAN
rs247963	UNQ1912	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:99896600-99933800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:99920000-99932800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:99920200-99933600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr5:99930800-99932200	Enhancers	Dnd41	blood
5	chr5:99931000-99932000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:99931000-99932200	Enhancers	Fetal Muscle Leg	muscle
7	chr5:99931000-99933800	Enhancers	Fetal Intestine Large	intestine
8	chr5:99931400-99932000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:99931400-99932000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:99931400-99932200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr5:99931400-99932200	Enhancers	Ovary	ovary
12	chr5:99931600-99932000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr5:99931600-99932200	Flanking Active TSS	HSMMtube	muscle
14	chr5:99931600-99934800	Weak transcription	Aorta	Aorta
15	chr5:99931800-99932000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:99931800-99932000	Weak transcription	Psoas Muscle	Psoas
17	chr5:99931800-99932000	Enhancers	NHEK	skin
18	chr5:99931800-99932000	Enhancers	NHLF	lung
19	chr5:99931800-99932200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:99931800-99932200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:99931800-99932200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr5:99931800-99932200	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr5:99931800-99932200	Enhancers	HUVEC	blood vessel
24	chr5:99931800-99932200	Enhancers	NH-A	brain
25	chr5:99931800-99932200	Enhancers	NHDF-Ad	bronchial
26	chr5:99931800-99932400	Enhancers	HSMM	muscle
27	chr5:99931800-99932400	Enhancers	Osteobl	bone

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