Variant report

Variant	rs28696257
Chromosome Location	chr7:121150950-121150951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM3C-3	chr7:121150830-121151324	NONHSAT123008

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10228676	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233243	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10237611	0.81[ASN][1000 genomes]
rs10240973	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253256	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10258260	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10258506	0.98[ASN][1000 genomes]
rs10258640	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10259325	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10270561	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10480752	0.81[ASN][1000 genomes]
rs10953936	0.95[ASN][1000 genomes]
rs10953937	0.91[ASN][1000 genomes]
rs11761290	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535189	0.85[ASN][1000 genomes]
rs12540408	0.83[ASN][1000 genomes]
rs13229583	0.81[ASN][1000 genomes]
rs1406194	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1528352	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1881374	0.93[ASN][1000 genomes]
rs1881375	0.97[ASN][1000 genomes]
rs1881376	0.97[ASN][1000 genomes]
rs1919086	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1983493	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1983494	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1983495	0.98[ASN][1000 genomes]
rs1983496	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049702	0.98[ASN][1000 genomes]
rs2103298	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103299	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141364	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178188	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485397	0.83[ASN][1000 genomes]
rs28578522	0.83[ASN][1000 genomes]
rs34843814	0.94[ASN][1000 genomes]
rs3847091	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847092	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857836	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727933	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4731023	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731024	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731025	0.98[ASN][1000 genomes]
rs6953922	0.92[ASN][1000 genomes]
rs6954048	0.94[ASN][1000 genomes]
rs6960065	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7777295	0.98[ASN][1000 genomes]
rs7777787	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787312	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7791746	0.98[ASN][1000 genomes]
rs7793736	0.86[ASN][1000 genomes]
rs7795140	0.83[ASN][1000 genomes]
rs867706	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649443	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9719308	0.87[EUR][1000 genomes]
rs9719756	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	25 gene(s)	inside rSNPs	diseases
2	nsv1026322	chr7:120841937-121188037	Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv539102	chr7:120841937-121188037	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1032054	chr7:120926379-121432971	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv539103	chr7:120926379-121432971	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv428507	chr7:121037303-121191934	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv608333	chr7:121132213-121379616	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:121149200-121152600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
2	chr7:121149800-121151400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:121150200-121152200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
4	chr7:121150400-121151600	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:121150400-121151600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:121150400-121151600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr7:121150600-121151400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
8	chr7:121150600-121151400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr7:121150600-121151400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:121150600-121151400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:121150600-121151600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
12	chr7:121150600-121152800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
13	chr7:121150800-121151200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:121150800-121151400	ZNF genes & repeats	Adipose Nuclei	Adipose
15	chr7:121150800-121152400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:121150800-121152600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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