Variant report

Variant	rs6781221
Chromosome Location	chr3:158998309-158998310
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr3:158998180-158998489	SK-N-SH_RA	brain:	n/a	n/a
2	RAD21	chr3:158998250-158998463	SK-N-SH_RA	brain:	n/a	n/a
3	GATA3	chr3:158998010-158998589	SH-SY5Y	brain:	n/a	n/a
4	EP300	chr3:158998096-158998729	SK-N-SH_RA	brain:	n/a	n/a
5	EP300	chr3:158998008-158998646	SK-N-SH_RA	brain:	n/a	n/a
6	EP300	chr3:158997659-158999016	SK-N-SH	brain:	n/a	n/a
7	GATA2	chr3:158997786-158998990	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158998052..159000120-chr3:159030298..159031893,2	K562	blood:
2	chr3:158991788..158993700-chr3:158997368..159000280,2	MCF-7	breast:

Variant related genes	Relation type
MIR3919	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10513537	0.82[ASW][hapmap];0.90[GIH][hapmap]
rs10936173	1.00[ASW][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap]
rs10936175	1.00[YRI][hapmap]
rs10936176	1.00[YRI][hapmap]
rs1122205	0.81[CEU][hapmap]
rs11924990	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13326945	0.86[GIH][hapmap]
rs1349165	0.81[CEU][hapmap]
rs1349166	0.81[CEU][hapmap]
rs1449018	0.81[CEU][hapmap]
rs1449019	0.81[CEU][hapmap]
rs1449021	0.87[AMR][1000 genomes]
rs1449025	0.81[CEU][hapmap]
rs1562669	0.81[CEU][hapmap]
rs1823311	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs1868414	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2122147	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2365490	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs2365820	0.87[CEU][hapmap]
rs6441253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs6441254	0.81[CEU][hapmap]
rs6777541	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap]
rs6791853	1.00[ASW][hapmap];0.91[GIH][hapmap];1.00[YRI][hapmap]
rs6807305	0.81[CEU][hapmap]
rs6810169	0.81[CEU][hapmap]
rs720397	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs7611870	0.81[CEU][hapmap]
rs7629577	0.81[CEU][hapmap]
rs7629583	0.81[CEU][hapmap]
rs7630467	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7639623	0.88[ASN][1000 genomes]
rs9283610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9283611	0.81[CEU][hapmap]
rs9290036	0.81[CEU][hapmap]
rs9681445	0.81[CEU][hapmap]
rs9809459	0.81[CEU][hapmap]
rs9820047	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9821641	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9823822	0.81[CEU][hapmap]
rs9825664	0.81[CEU][hapmap]
rs9827242	0.84[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9827400	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9829189	0.87[AMR][1000 genomes]
rs9831067	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[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]
rs9834328	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs9834337	0.81[CEU][hapmap]
rs9838646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs9839112	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9852196	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9855118	0.81[CEU][hapmap]
rs9856166	1.00[ASW][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap]
rs9862769	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9867432	0.80[CEU][hapmap]
rs9873091	0.81[CEU][hapmap]
rs9874862	0.81[CEU][hapmap]
rs9880642	0.90[CHB][hapmap]

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	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1012602	chr3:158800182-159031618	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158997600-158999200	Enhancers	Brain Germinal Matrix	brain
2	chr3:158997800-158998600	Enhancers	Fetal Brain Female	brain
3	chr3:158997800-158999000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:158997800-158999200	Enhancers	Adipose Nuclei	Adipose
5	chr3:158997800-158999200	Enhancers	Fetal Brain Male	brain
6	chr3:158998000-158998800	Enhancers	Brain Cingulate Gyrus	brain
7	chr3:158998000-158999000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:158998200-158998800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:158998200-158999200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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