Variant report

Variant	rs66698345
Chromosome Location	chr3:112322531-112322532
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112321970..112325392-chr3:112326276..112329430,4	K562	blood:

Variant related genes	Relation type
ENSG00000091986	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10511317	0.82[EUR][1000 genomes]
rs11919639	0.86[EUR][1000 genomes]
rs11921669	0.86[EUR][1000 genomes]
rs13059364	0.89[EUR][1000 genomes]
rs13063173	0.89[EUR][1000 genomes]
rs13064534	0.83[EUR][1000 genomes]
rs13065703	0.89[EUR][1000 genomes]
rs13070342	0.89[EUR][1000 genomes]
rs13071492	0.89[EUR][1000 genomes]
rs13080547	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080749	0.89[EUR][1000 genomes]
rs13081201	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081265	0.85[EUR][1000 genomes]
rs13081632	0.85[EUR][1000 genomes]
rs13088339	0.96[EUR][1000 genomes]
rs13088349	0.96[EUR][1000 genomes]
rs13088467	0.96[EUR][1000 genomes]
rs13092057	0.82[EUR][1000 genomes]
rs13094161	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13094649	0.89[EUR][1000 genomes]
rs13095000	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096943	0.85[EUR][1000 genomes]
rs16845067	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16859661	0.85[EUR][1000 genomes]
rs16859727	0.89[EUR][1000 genomes]
rs16859758	0.89[EUR][1000 genomes]
rs16859775	0.83[ASN][1000 genomes]
rs16859779	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16859787	0.96[EUR][1000 genomes]
rs16859793	0.96[EUR][1000 genomes]
rs1994711	0.81[AMR][1000 genomes]
rs2220656	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705526	0.82[EUR][1000 genomes]
rs28365853	0.96[EUR][1000 genomes]
rs2942062	0.81[AMR][1000 genomes]
rs34080815	0.89[EUR][1000 genomes]
rs34139211	0.89[EUR][1000 genomes]
rs34248586	0.89[EUR][1000 genomes]
rs34284082	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34541731	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34596334	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34597203	0.89[EUR][1000 genomes]
rs34645913	0.89[EUR][1000 genomes]
rs34829517	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34889961	0.89[EUR][1000 genomes]
rs34949685	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34962178	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35107041	0.86[EUR][1000 genomes]
rs35240469	0.89[EUR][1000 genomes]
rs35255669	0.96[EUR][1000 genomes]
rs35349986	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35512450	0.89[EUR][1000 genomes]
rs35526995	0.89[EUR][1000 genomes]
rs35529363	0.96[EUR][1000 genomes]
rs35692417	0.96[EUR][1000 genomes]
rs35709173	0.96[EUR][1000 genomes]
rs35725070	0.89[EUR][1000 genomes]
rs35748518	0.89[EUR][1000 genomes]
rs35803911	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35840933	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35931975	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36025914	0.96[EUR][1000 genomes]
rs36045008	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36061184	0.96[EUR][1000 genomes]
rs36146261	0.96[EUR][1000 genomes]
rs36153507	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736269	0.89[EUR][1000 genomes]
rs3736270	0.89[EUR][1000 genomes]
rs3736271	0.89[EUR][1000 genomes]
rs3773698	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3773701	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3773704	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3773706	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3773710	0.96[EUR][1000 genomes]
rs3821684	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55742760	0.96[EUR][1000 genomes]
rs56662636	0.89[EUR][1000 genomes]
rs56856838	0.89[EUR][1000 genomes]
rs56970524	0.96[EUR][1000 genomes]
rs57346109	0.89[EUR][1000 genomes]
rs58891772	0.89[EUR][1000 genomes]
rs59242272	0.95[AFR][1000 genomes]
rs59279185	0.89[EUR][1000 genomes]
rs59858117	0.89[EUR][1000 genomes]
rs60321074	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60646325	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66486470	0.89[EUR][1000 genomes]
rs66791711	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66910014	0.89[EUR][1000 genomes]
rs67021100	0.85[EUR][1000 genomes]
rs67204151	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67513863	0.93[EUR][1000 genomes]
rs67940544	0.96[EUR][1000 genomes]
rs67944354	0.89[EUR][1000 genomes]
rs71317505	0.82[EUR][1000 genomes]
rs71317506	0.85[EUR][1000 genomes]
rs71317507	0.89[EUR][1000 genomes]
rs71317508	0.89[EUR][1000 genomes]
rs71317510	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724125	0.96[EUR][1000 genomes]
rs72942070	0.92[AFR][1000 genomes]
rs73229350	0.89[EUR][1000 genomes]
rs73229353	0.89[EUR][1000 genomes]
rs73229398	0.96[EUR][1000 genomes]
rs958935	0.96[EUR][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	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats 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	39 gene(s)	inside rSNPs	diseases
3	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs66698345	SLC35A5	cis	Thyroid	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112281800-112324200	Weak transcription	Spleen	Spleen
2	chr3:112281800-112325400	Weak transcription	Gastric	stomach
3	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
5	chr3:112282400-112322800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:112282400-112324200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:112298600-112325200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:112298800-112335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:112300200-112331000	Weak transcription	Lung	lung
11	chr3:112300200-112334000	Weak transcription	Fetal Stomach	stomach
12	chr3:112302600-112322800	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:112302800-112324200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:112303600-112322800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:112303800-112324200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr3:112305000-112324200	Weak transcription	Fetal Brain Male	brain
17	chr3:112305200-112323000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:112305200-112323600	Weak transcription	Brain Substantia Nigra	brain
19	chr3:112305400-112323400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:112305400-112324000	Weak transcription	Brain Anterior Caudate	brain
21	chr3:112305400-112330400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:112305600-112324200	Weak transcription	Fetal Kidney	kidney
23	chr3:112305800-112334800	Weak transcription	Aorta	Aorta
24	chr3:112307400-112329000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:112311600-112330600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:112311600-112331000	Weak transcription	Psoas Muscle	Psoas
27	chr3:112312400-112324200	Weak transcription	Ovary	ovary
28	chr3:112312400-112325200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:112312400-112326800	Weak transcription	Fetal Lung	lung
30	chr3:112312400-112331000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:112312600-112323000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:112312600-112323400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:112312600-112323600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:112312600-112323600	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:112312600-112324200	Weak transcription	Brain Angular Gyrus	brain
36	chr3:112312600-112330400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:112312600-112346200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:112312600-112347200	Weak transcription	Fetal Intestine Large	intestine
39	chr3:112316000-112327400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:112316200-112323600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:112316200-112342800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr3:112316400-112323400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:112316400-112333600	Weak transcription	A549	lung
44	chr3:112316600-112337600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:112316800-112323000	Weak transcription	NHDF-Ad	bronchial
46	chr3:112316800-112323600	Weak transcription	Primary T cells from cord blood	blood
47	chr3:112317000-112324200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:112317200-112322600	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr3:112317600-112322600	Weak transcription	Adipose Nuclei	Adipose
50	chr3:112317600-112328600	Weak transcription	Stomach Smooth Muscle	stomach

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