Variant report

Variant	rs9871660
Chromosome Location	chr3:67787897-67787898
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM19A1-2	chr3:67787799-67788216	l_2384_chr3:67787798-67880076_thyroid

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10428091	0.92[ASN][1000 genomes]
rs10428122	0.91[ASN][1000 genomes]
rs11127733	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12330732	0.83[ASN][1000 genomes]
rs13067333	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1459912	0.95[ASN][1000 genomes]
rs1459913	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1459918	0.88[ASN][1000 genomes]
rs1459919	0.88[ASN][1000 genomes]
rs1585384	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1599209	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2125810	0.94[ASN][1000 genomes]
rs2125812	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2125813	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2169110	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2169111	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2169113	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2362440	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2362449	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34134719	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34520011	0.88[ASN][1000 genomes]
rs35194427	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4350935	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4856889	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4856890	0.87[ASN][1000 genomes]
rs6768970	0.87[ASN][1000 genomes]
rs6798796	0.89[ASN][1000 genomes]
rs68005467	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7618120	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7642815	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9824545	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9833922	0.87[ASN][1000 genomes]
rs9855740	0.88[ASN][1000 genomes]
rs9857889	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9871777	0.88[ASN][1000 genomes]
rs993597	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	esv3359258	chr3:67589615-67828274	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67721400-67800400	Weak transcription	Left Ventricle	heart
2	chr3:67775800-67790200	Weak transcription	Psoas Muscle	Psoas
3	chr3:67785600-67788200	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr3:67785800-67790000	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr3:67785800-67791600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr3:67786000-67790000	Enhancers	Primary T cells fromperipheralblood	blood
7	chr3:67786000-67791600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr3:67786200-67788400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:67786200-67790200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:67786600-67790000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:67787400-67788200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr3:67787400-67788400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:67787600-67788000	Enhancers	Primary T cells from cord blood	blood
14	chr3:67787600-67788800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr3:67787600-67788800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr3:67787600-67789200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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