Variant report

Variant	rs9861721
Chromosome Location	chr3:118695258-118695259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10212391	0.82[YRI][hapmap];0.95[AFR][1000 genomes]
rs10488303	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11923277	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12491204	0.82[CHB][hapmap]
rs16829165	0.83[AFR][1000 genomes]
rs16829203	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16829206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16829250	0.84[CHD][hapmap];1.00[GIH][hapmap]
rs17491031	0.90[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2160054	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs2866319	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[EUR][1000 genomes]
rs41330049	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41414745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41523948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611809	0.87[AFR][1000 genomes]
rs56314531	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6785161	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6795523	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72966889	0.85[AFR][1000 genomes]
rs72968610	0.84[AFR][1000 genomes]
rs7629089	0.82[AFR][1000 genomes]
rs7633584	0.86[LWK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs7644623	0.92[ASW][hapmap];0.87[GIH][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs9817851	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9817943	0.84[AFR][1000 genomes]
rs9834188	0.90[AFR][1000 genomes]
rs9836742	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9837571	0.81[ASW][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes]
rs9847272	0.89[LWK][hapmap];0.83[AFR][1000 genomes]
rs9854240	0.95[AFR][1000 genomes]
rs9860173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867214	0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs9874337	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv1010475	chr3:118657382-118789714	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv877369	chr3:118681771-118824418	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv2756586	chr3:118688611-118863998	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118683400-118696200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:118688800-118706000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:118689000-118703600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:118692200-118696200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:118692200-118696800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:118692200-118700400	Weak transcription	Brain Angular Gyrus	brain
7	chr3:118692400-118695600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:118692600-118704400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:118692800-118696000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:118693400-118696000	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:118693400-118696400	Weak transcription	HSMMtube	muscle
12	chr3:118693400-118704400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:118693800-118695400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:118694000-118696400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:118694000-118696400	Weak transcription	Brain Substantia Nigra	brain
16	chr3:118695200-118695800	Enhancers	Primary T cells from cord blood	blood
17	chr3:118695200-118697600	Enhancers	Brain Anterior Caudate	brain

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