Variant report

Variant	rs12669878
Chromosome Location	chr7:128203134-128203135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12668292	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12670251	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12671449	0.80[EUR][1000 genomes]
rs12671633	0.80[EUR][1000 genomes]
rs1839595	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34648097	0.82[EUR][1000 genomes]
rs4448212	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490755	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4530963	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4731485	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56010148	0.81[AMR][1000 genomes]
rs56199722	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56329212	0.80[EUR][1000 genomes]
rs58210776	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59475830	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59955357	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61031958	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61479217	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62481136	0.80[EUR][1000 genomes]
rs62481142	0.80[EUR][1000 genomes]
rs62481155	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62481886	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62481894	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62481898	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62481925	0.80[AMR][1000 genomes]
rs62481947	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62483264	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62483275	0.87[EUR][1000 genomes]
rs62483280	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62483285	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62483299	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62483349	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62483350	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6946411	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6973650	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73236051	0.83[EUR][1000 genomes]
rs7799914	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7809300	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9689994	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9690750	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12669878	RP11-274B21.4	cis	Adipose Subcutaneous	GTEx
rs12669878	RP11-274B21.1	cis	Adipose Subcutaneous	GTEx
rs12669878	RP11-274B21.2	cis	Adipose Subcutaneous	GTEx
rs12669878	RP11-274B21.4	cis	Whole Blood	GTEx
rs12669878	RP11-274B21.4	cis	Nerve Tibial	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128172600-128210800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:128172600-128214800	Weak transcription	Gastric	stomach
3	chr7:128172800-128239800	Weak transcription	Small Intestine	intestine
4	chr7:128173000-128231800	Weak transcription	Colonic Mucosa	Colon
5	chr7:128173000-128231800	Weak transcription	Fetal Kidney	kidney
6	chr7:128173600-128214800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:128173800-128214800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr7:128173800-128234400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:128174000-128210600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr7:128174000-128220600	Weak transcription	NHLF	lung
11	chr7:128174000-128231800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr7:128174000-128232600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:128175400-128231800	Weak transcription	Left Ventricle	heart
14	chr7:128176000-128214800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr7:128177600-128231800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:128179200-128231800	Weak transcription	Esophagus	oesophagus
17	chr7:128181800-128231800	Weak transcription	Aorta	Aorta
18	chr7:128183000-128214200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr7:128183400-128214800	Weak transcription	HUVEC	blood vessel
20	chr7:128183600-128214800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr7:128185000-128210600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr7:128185200-128210000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr7:128187400-128212400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr7:128187400-128214800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr7:128187400-128214800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr7:128187600-128205200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr7:128187600-128213800	Weak transcription	Osteobl	bone
28	chr7:128187600-128214400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr7:128187600-128232000	Weak transcription	NH-A	brain
30	chr7:128187800-128214800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr7:128188000-128208800	Weak transcription	K562	blood
32	chr7:128188000-128210800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr7:128188000-128213800	Weak transcription	Brain Anterior Caudate	brain
34	chr7:128188000-128213800	Weak transcription	Brain Hippocampus Middle	brain
35	chr7:128188000-128214800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr7:128188000-128214800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr7:128188000-128215000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:128188000-128215000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:128188000-128220800	Weak transcription	NHEK	skin
40	chr7:128188000-128232800	Weak transcription	Fetal Brain Female	brain
41	chr7:128188200-128215000	Weak transcription	Hela-S3	cervix
42	chr7:128188200-128229800	Weak transcription	HSMM	muscle
43	chr7:128188400-128209000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:128188400-128210000	Weak transcription	Placenta	Placenta
45	chr7:128188400-128210400	Weak transcription	Primary B cells from cord blood	blood
46	chr7:128188400-128210400	Weak transcription	Fetal Lung	lung
47	chr7:128188400-128210600	Weak transcription	Spleen	Spleen
48	chr7:128188400-128212400	Weak transcription	Lung	lung
49	chr7:128188400-128214800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr7:128188400-128230800	Weak transcription	Primary T cells from cord blood	blood

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