Variant report

Variant	rs56403867
Chromosome Location	chr7:128200537-128200538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10240961	0.84[EUR][1000 genomes]
rs10273146	0.93[EUR][1000 genomes]
rs10954188	0.93[ASN][1000 genomes]
rs10954208	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11763357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532347	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12534956	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535956	0.88[EUR][1000 genomes]
rs13247422	0.93[EUR][1000 genomes]
rs2003954	0.83[AMR][1000 genomes]
rs2013189	0.83[AMR][1000 genomes]
rs2060718	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57185253	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58709686	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58781928	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60117311	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61310483	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62481140	0.85[EUR][1000 genomes]
rs62481159	0.92[EUR][1000 genomes]
rs62481882	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62481884	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62481903	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62481943	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62483279	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62483283	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62483292	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62483294	0.84[ASN][1000 genomes]
rs62483312	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6969473	0.80[ASN][1000 genomes]
rs73723614	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs56403867	RP11-274B21.4	cis	Nerve Tibial	GTEx
rs56403867	RP11-274B21.4	cis	lung	GTEx
rs56403867	CICP14	cis	Thyroid	GTEx
rs56403867	RP11-274B21.2	cis	Thyroid	GTEx

Chromatin state (count:108 , 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	chr7:128173600-128201000	Weak transcription	Psoas Muscle	Psoas
7	chr7:128173600-128214800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:128173800-128201000	Weak transcription	Brain Germinal Matrix	brain
9	chr7:128173800-128214800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:128173800-128234400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:128174000-128210600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr7:128174000-128220600	Weak transcription	NHLF	lung
13	chr7:128174000-128231800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr7:128174000-128232600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr7:128175400-128231800	Weak transcription	Left Ventricle	heart
16	chr7:128176000-128214800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr7:128177600-128231800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr7:128179200-128231800	Weak transcription	Esophagus	oesophagus
19	chr7:128181800-128231800	Weak transcription	Aorta	Aorta
20	chr7:128183000-128201000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:128183000-128214200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr7:128183400-128214800	Weak transcription	HUVEC	blood vessel
23	chr7:128183600-128214800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr7:128185000-128210600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr7:128185200-128210000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr7:128187400-128212400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr7:128187400-128214800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr7:128187400-128214800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:128187600-128205200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr7:128187600-128213800	Weak transcription	Osteobl	bone
31	chr7:128187600-128214400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr7:128187600-128232000	Weak transcription	NH-A	brain
33	chr7:128187800-128214800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr7:128188000-128208800	Weak transcription	K562	blood
35	chr7:128188000-128210800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr7:128188000-128213800	Weak transcription	Brain Anterior Caudate	brain
37	chr7:128188000-128213800	Weak transcription	Brain Hippocampus Middle	brain
38	chr7:128188000-128214800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr7:128188000-128214800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr7:128188000-128215000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:128188000-128215000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:128188000-128220800	Weak transcription	NHEK	skin
43	chr7:128188000-128232800	Weak transcription	Fetal Brain Female	brain
44	chr7:128188200-128215000	Weak transcription	Hela-S3	cervix
45	chr7:128188200-128229800	Weak transcription	HSMM	muscle
46	chr7:128188400-128201200	Weak transcription	GM12878-XiMat	blood
47	chr7:128188400-128209000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr7:128188400-128210000	Weak transcription	Placenta	Placenta
49	chr7:128188400-128210400	Weak transcription	Primary B cells from cord blood	blood
50	chr7:128188400-128210400	Weak transcription	Fetal Lung	lung

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