Variant report

Variant	rs2235
Chromosome Location	chr3:67729534-67729535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10510966	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706254	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11716677	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11718788	0.88[ASN][1000 genomes]
rs13060205	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062710	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13078350	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13087072	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094934	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1376030	0.81[JPT][hapmap]
rs1473351	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1563808	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6548721	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6770260	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6773969	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6781799	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7625814	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7632886	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7640220	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9824834	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9863391	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]

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	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	nsv876922	chr3:67635506-67755257	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv428739	chr3:67656829-67730379	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers 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	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2235	RP11-81N13.1	cis	Thyroid	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67705600-67756200	Weak transcription	Aorta	Aorta
2	chr3:67705800-67776000	Weak transcription	Ovary	ovary
3	chr3:67717200-67730800	Weak transcription	Gastric	stomach
4	chr3:67721200-67759200	Weak transcription	Psoas Muscle	Psoas
5	chr3:67721400-67800400	Weak transcription	Left Ventricle	heart
6	chr3:67727600-67747600	Weak transcription	A549	lung
7	chr3:67727800-67730000	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr3:67727800-67755000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:67728000-67730600	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr3:67728000-67730600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr3:67728000-67730600	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr3:67728200-67730000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr3:67728200-67730600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:67728400-67729600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr3:67728400-67730000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:67728400-67730800	Enhancers	Primary T cells fromperipheralblood	blood
17	chr3:67728600-67730000	Enhancers	Fetal Thymus	thymus
18	chr3:67728800-67729800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:67728800-67729800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:67728800-67730800	Enhancers	Primary B cells from peripheral blood	blood
21	chr3:67729000-67730200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:67729000-67730200	Enhancers	GM12878-XiMat	blood
23	chr3:67729200-67729800	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr3:67729200-67729800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:67729200-67731000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:67729400-67729800	Weak transcription	Primary B cells from cord blood	blood

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