Variant report

Variant	rs12534956
Chromosome Location	chr7:128239545-128239546
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10273146	0.89[EUR][1000 genomes]
rs10954188	0.93[ASN][1000 genomes]
rs10954208	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11763357	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532347	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12535956	0.85[EUR][1000 genomes]
rs13247422	0.89[EUR][1000 genomes]
rs2003954	0.87[AMR][1000 genomes]
rs2013189	0.87[AMR][1000 genomes]
rs2060718	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56403867	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57185253	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58709686	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58781928	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60117311	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61310483	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62481140	0.83[EUR][1000 genomes]
rs62481159	0.88[EUR][1000 genomes]
rs62481882	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62481884	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62481903	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62481943	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62483279	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62483283	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62483292	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62483294	0.84[ASN][1000 genomes]
rs62483312	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6969473	0.80[ASN][1000 genomes]
rs73723614	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12534956	RP11-274B21.2	cis	Thyroid	GTEx
rs12534956	RP11-274B21.4	cis	lung	GTEx
rs12534956	CICP14	cis	Thyroid	GTEx
rs12534956	RP11-274B21.4	cis	Nerve Tibial	GTEx

Chromatin state (count:117 , 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	chr7:128233400-128249200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:128233400-128249200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr7:128233400-128249200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr7:128233400-128249200	Weak transcription	Fetal Kidney	kidney
19	chr7:128233400-128249200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr7:128233400-128249200	Weak transcription	HUVEC	blood vessel
21	chr7:128233400-128249200	Weak transcription	NH-A	brain
22	chr7:128233400-128249200	Weak transcription	NHLF	lung
23	chr7:128233400-128258400	Weak transcription	Thymus	Thymus
24	chr7:128233400-128258600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:128233400-128258800	Weak transcription	Aorta	Aorta
26	chr7:128233400-128258800	Weak transcription	Esophagus	oesophagus
27	chr7:128233400-128258800	Weak transcription	Spleen	Spleen
28	chr7:128233400-128259000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr7:128233400-128259000	Weak transcription	Colon Smooth Muscle	Colon
30	chr7:128233400-128259600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr7:128233400-128272000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:128233600-128249200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:128233600-128249200	Weak transcription	GM12878-XiMat	blood
34	chr7:128233600-128258800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr7:128233800-128239600	Weak transcription	Adipose Nuclei	Adipose
36	chr7:128233800-128257600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr7:128233800-128258800	Weak transcription	Fetal Brain Female	brain
38	chr7:128234400-128249200	Weak transcription	HSMM	muscle
39	chr7:128234400-128249400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr7:128234600-128246400	Weak transcription	Fetal Intestine Large	intestine
41	chr7:128234600-128249200	Weak transcription	Hela-S3	cervix
42	chr7:128234600-128257600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr7:128234600-128258800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr7:128234600-128258800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr7:128234600-128258800	Weak transcription	Gastric	stomach
46	chr7:128234600-128271200	Weak transcription	Fetal Lung	lung
47	chr7:128234800-128239600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:128235000-128253800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr7:128235200-128249200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr7:128235400-128249200	Weak transcription	Osteobl	bone

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