Variant report

Variant	rs7639293
Chromosome Location	chr3:67998018-67998019
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:67991094..67994023-chr3:67995213..67998211,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM19A1-1	chr3:67997565-67998137	ENSG00000241316
2	lnc-FAM19A1-1	chr3:67997565-67998136	NR_109992

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10510968	0.85[ASN][1000 genomes]
rs1349006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1385522	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1447749	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1447753	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1447754	0.92[ASN][1000 genomes]
rs1447761	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1447771	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1550915	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1564870	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17140740	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17140869	0.87[ASN][1000 genomes]
rs1839042	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1872433	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1905800	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1905801	0.91[AFR][1000 genomes]
rs2121779	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2361332	0.80[ASN][1000 genomes]
rs2361371	0.85[ASN][1000 genomes]
rs2885251	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs34597575	0.82[ASN][1000 genomes]
rs35040857	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs35976744	0.96[ASN][1000 genomes]
rs36112959	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4103349	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4376054	0.85[ASN][1000 genomes]
rs4603969	0.83[ASN][1000 genomes]
rs4856914	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4856916	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4856920	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4856931	0.91[ASN][1000 genomes]
rs6763163	0.89[ASN][1000 genomes]
rs6771729	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6775637	0.89[ASN][1000 genomes]
rs6778007	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6784552	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6790710	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6790969	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6808564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7609730	0.86[ASN][1000 genomes]
rs7615755	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7629362	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7630186	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7635638	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7643788	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7649361	0.91[AFR][1000 genomes]
rs7649759	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs936779	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002010	chr3:67785913-68312064	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv834720	chr3:67853167-68037201	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1009871	chr3:67862617-68312064	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv536583	chr3:67862617-68312064	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1010231	chr3:67894825-68117879	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1013531	chr3:67917771-68070027	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv3442201	chr3:67925312-68064610	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3338669	chr3:67925912-68064160	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv876923	chr3:67938089-68016333	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv3395568	chr3:67955462-68064660	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv876924	chr3:67978367-68063259	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67990400-67998800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:67994200-67998200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:67996600-67998200	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr3:67996800-67998400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:67997000-67998200	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr3:67997000-67998200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr3:67997000-67998400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:67997000-67998400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr3:67997000-67998400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr3:67997800-67998200	Enhancers	Primary T cells fromperipheralblood	blood
11	chr3:67997800-67998200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:67998000-67998200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr3:67998000-67998200	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr3:67998000-67998200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr3:67998000-67998400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:67998000-67998400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:67998000-67998800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:67998000-67999200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

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