Variant report

Variant	rs35438259
Chromosome Location	chr5:68606611-68606612
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TAF9-3	chr5:68603495-68607031	NONHSAT101909

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10940215	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11741775	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11741826	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11742878	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11745537	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11745591	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11749723	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11750525	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11957698	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12189282	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13154469	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13168973	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28499200	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34449757	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34862981	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35316810	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4288083	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62373182	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66514959	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs68083627	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6865481	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6869305	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6877725	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6881767	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6893648	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72767881	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35438259	CCDC125	cis	Thyroid	GTEx
rs35438259	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs35438259	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs35438259	CCDC125	cis	lung	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
2	chr5:68564200-68611200	Weak transcription	Fetal Brain Male	brain
3	chr5:68565600-68627400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:68566800-68610800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:68575600-68608200	Weak transcription	Right Ventricle	heart
6	chr5:68576200-68609400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:68576400-68614400	Weak transcription	Colon Smooth Muscle	Colon
8	chr5:68576400-68627600	Weak transcription	Brain Substantia Nigra	brain
9	chr5:68576400-68627800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr5:68576600-68627800	Weak transcription	Brain Angular Gyrus	brain
11	chr5:68577400-68607800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr5:68577400-68628200	Weak transcription	Small Intestine	intestine
13	chr5:68577600-68619800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr5:68577600-68627400	Weak transcription	NHEK	skin
15	chr5:68577800-68626600	Weak transcription	A549	lung
16	chr5:68581600-68627600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:68581800-68608200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr5:68581800-68609000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:68581800-68609200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr5:68581800-68611000	Weak transcription	Psoas Muscle	Psoas
21	chr5:68581800-68617800	Weak transcription	Brain Hippocampus Middle	brain
22	chr5:68581800-68626800	Weak transcription	Fetal Brain Female	brain
23	chr5:68581800-68627600	Weak transcription	Brain Anterior Caudate	brain
24	chr5:68582800-68622400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:68585000-68609000	Weak transcription	Spleen	Spleen
26	chr5:68588600-68615800	Weak transcription	Colonic Mucosa	Colon
27	chr5:68591600-68609200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:68591600-68614000	Weak transcription	Osteobl	bone
29	chr5:68591600-68627600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:68596000-68626800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:68596600-68607800	Weak transcription	Esophagus	oesophagus
32	chr5:68596600-68612800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr5:68597000-68608800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr5:68597000-68611400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:68597200-68608000	Weak transcription	Fetal Stomach	stomach
36	chr5:68598600-68611000	Strong transcription	Liver	Liver
37	chr5:68598800-68606800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr5:68599400-68612000	Weak transcription	HepG2	liver
39	chr5:68599600-68627800	Weak transcription	NH-A	brain
40	chr5:68600600-68610000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr5:68600800-68609000	Weak transcription	NHLF	lung
42	chr5:68600800-68610000	Strong transcription	Primary T cells from cord blood	blood
43	chr5:68601400-68627600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr5:68601800-68608800	Weak transcription	Aorta	Aorta
45	chr5:68602400-68608000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr5:68602400-68611400	Weak transcription	Fetal Muscle Leg	muscle
47	chr5:68603800-68609200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:68604000-68608400	Weak transcription	Placenta	Placenta
49	chr5:68604200-68609600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:68605200-68607400	Strong transcription	Fetal Intestine Large	intestine

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