Variant report

Variant	rs10233059
Chromosome Location	chr7:128239321-128239322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10085435	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224862	0.82[EUR][1000 genomes]
rs10227608	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10231136	0.80[AFR][1000 genomes]
rs10241185	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10250369	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253131	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10259359	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10261037	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10269844	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270431	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10270985	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10272840	0.82[AFR][1000 genomes]
rs10274878	0.83[AMR][1000 genomes]
rs10276810	0.80[EUR][1000 genomes]
rs10954205	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11760285	1.00[ASN][1000 genomes]
rs11761312	0.83[AMR][1000 genomes]
rs11766319	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768485	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11769546	1.00[ASN][1000 genomes]
rs11771884	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12333625	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12535238	0.82[EUR][1000 genomes]
rs12537208	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13224613	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13233377	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13235219	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13237593	0.86[AMR][1000 genomes]
rs13246302	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28496126	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28521260	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28521711	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs339079	0.80[EUR][1000 genomes]
rs339093	0.82[EUR][1000 genomes]
rs34120723	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34125589	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34490491	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34751214	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34757247	0.89[AFR][1000 genomes]
rs34887739	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34942906	0.88[AFR][1000 genomes]
rs34960471	0.88[AFR][1000 genomes]
rs35247963	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35603038	0.93[AFR][1000 genomes]
rs35825132	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35871589	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3816421	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4289745	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55953818	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60029447	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60654313	0.85[AFR][1000 genomes]
rs6467181	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467184	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467201	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6467205	0.82[EUR][1000 genomes]
rs6943737	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6946179	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6958343	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960296	0.89[EUR][1000 genomes]
rs6961754	0.85[EUR][1000 genomes]
rs6963982	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967393	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6969343	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971819	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6972787	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6976879	0.82[EUR][1000 genomes]
rs6977126	0.82[EUR][1000 genomes]
rs71546785	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71546786	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71546790	0.92[AFR][1000 genomes]
rs71548762	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71578280	1.00[ASN][1000 genomes]
rs7776915	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7777625	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7778169	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7778731	0.81[EUR][1000 genomes]
rs7786772	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787764	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7790839	0.86[AFR][1000 genomes]
rs7798172	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804472	0.82[EUR][1000 genomes]
rs7810047	0.82[EUR][1000 genomes]
rs7811083	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9690225	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9690934	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9692416	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9768808	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9769753	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1848097	chr7:128179503-128248497	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv1810084	chr7:128201902-128248697	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv1829966	chr7:128201902-128248697	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1847512	chr7:128201902-128248697	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv966885	chr7:128212815-128256300	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10233059	RP11-274B21.10	cis	Thyroid	GTEx
rs10233059	METTL2B	cis	Artery Tibial	GTEx
rs10233059	CICP14	cis	Thyroid	GTEx
rs10233059	METTL2B	cis	Skin Sun Exposed Lower leg	GTEx
rs10233059	RP11-274B21.10	cis	Esophagus Muscularis	GTEx
rs10233059	CICP14	cis	lung	GTEx
rs10233059	CICP14	cis	Muscle Skeletal	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128172800-128239800	Weak transcription	Small Intestine	intestine
2	chr7:128197800-128241800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:128200000-128258800	Weak transcription	Right Ventricle	heart
4	chr7:128204800-128258800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr7:128217800-128244000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr7:128219400-128249200	Weak transcription	Fetal Heart	heart
7	chr7:128220800-128249200	Weak transcription	A549	lung
8	chr7:128223800-128258800	Weak transcription	Lung	lung
9	chr7:128226400-128258800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr7:128230000-128249200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:128230800-128240400	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr7:128231000-128241800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:128233200-128258800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:128233200-128258800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:128233400-128239400	Weak transcription	Colonic Mucosa	Colon
16	chr7:128233400-128249200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr7:128233400-128249200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr7:128233400-128249200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr7:128233400-128249200	Weak transcription	Fetal Kidney	kidney
20	chr7:128233400-128249200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr7:128233400-128249200	Weak transcription	HUVEC	blood vessel
22	chr7:128233400-128249200	Weak transcription	NH-A	brain
23	chr7:128233400-128249200	Weak transcription	NHLF	lung
24	chr7:128233400-128258400	Weak transcription	Thymus	Thymus
25	chr7:128233400-128258600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:128233400-128258800	Weak transcription	Aorta	Aorta
27	chr7:128233400-128258800	Weak transcription	Esophagus	oesophagus
28	chr7:128233400-128258800	Weak transcription	Spleen	Spleen
29	chr7:128233400-128259000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr7:128233400-128259000	Weak transcription	Colon Smooth Muscle	Colon
31	chr7:128233400-128259600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr7:128233400-128272000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:128233600-128249200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr7:128233600-128249200	Weak transcription	GM12878-XiMat	blood
35	chr7:128233600-128258800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr7:128233800-128239600	Weak transcription	Adipose Nuclei	Adipose
37	chr7:128233800-128257600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr7:128233800-128258800	Weak transcription	Fetal Brain Female	brain
39	chr7:128234400-128249200	Weak transcription	HSMM	muscle
40	chr7:128234400-128249400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr7:128234600-128246400	Weak transcription	Fetal Intestine Large	intestine
42	chr7:128234600-128249200	Weak transcription	Hela-S3	cervix
43	chr7:128234600-128257600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr7:128234600-128258800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr7:128234600-128258800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr7:128234600-128258800	Weak transcription	Gastric	stomach
47	chr7:128234600-128271200	Weak transcription	Fetal Lung	lung
48	chr7:128234800-128239600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr7:128235000-128253800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr7:128235200-128249200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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