Variant report

Variant	rs71546790
Chromosome Location	chr7:128289004-128289005
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM71F2-1	chr7:128288846-128289174	NONHSAT123218
2	lnc-FAM71F2-1	chr7:128288960-128289038	NONHSAT123221
3	lnc-FAM71F2-1	chr7:128288840-128289065	NONHSAT123217
4	lnc-FAM71F2-1	chr7:128288846-128289036	NONHSAT123222

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10085435	0.89[AFR][1000 genomes]
rs10227608	0.84[AFR][1000 genomes]
rs10233059	0.92[AFR][1000 genomes]
rs10250369	0.84[AFR][1000 genomes]
rs10253131	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10261037	0.85[AFR][1000 genomes]
rs10269844	0.86[AFR][1000 genomes]
rs10270431	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10954205	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11768485	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12333625	0.89[ASN][1000 genomes]
rs12536288	0.89[ASN][1000 genomes]
rs12537208	0.88[AFR][1000 genomes]
rs12706858	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13224613	0.89[ASN][1000 genomes]
rs13235219	0.89[ASN][1000 genomes]
rs28496126	0.88[AFR][1000 genomes]
rs28521260	0.84[AFR][1000 genomes]
rs28521711	1.00[ASN][1000 genomes]
rs34120723	0.89[ASN][1000 genomes]
rs34490491	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs34751214	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs34757247	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34942906	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34960471	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35603038	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35871589	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3816421	0.96[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4289745	0.89[ASN][1000 genomes]
rs55953818	0.88[AFR][1000 genomes]
rs60029447	0.86[AFR][1000 genomes]
rs6467184	0.86[AFR][1000 genomes]
rs6467201	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6958343	0.86[AFR][1000 genomes]
rs6960296	0.89[ASN][1000 genomes]
rs6961754	0.84[ASN][1000 genomes]
rs6967393	0.89[ASN][1000 genomes]
rs6969343	0.83[AFR][1000 genomes]
rs6971819	0.89[ASN][1000 genomes]
rs71546785	0.86[AFR][1000 genomes]
rs71546786	0.88[AFR][1000 genomes]
rs7776915	0.92[AFR][1000 genomes]
rs7778169	0.94[AFR][1000 genomes]
rs7787764	0.89[ASN][1000 genomes]
rs7790478	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7798172	0.88[AFR][1000 genomes]
rs7811083	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9690225	0.86[AFR][1000 genomes]
rs9690934	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9692416	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9768808	0.89[ASN][1000 genomes]
rs9769753	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv970938	chr7:128256300-128300276	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv981680	chr7:128288269-128298277	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs71546790	RP11-274B21.10	cis	Esophagus Muscularis	GTEx
rs71546790	CICP14	cis	Muscle Skeletal	GTEx
rs71546790	CALU	cis	frontal cortex	BrainEAC

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128237800-128290400	Weak transcription	HepG2	liver
2	chr7:128239200-128296400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:128242600-128292800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:128249600-128293400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr7:128249600-128295200	Weak transcription	NH-A	brain
6	chr7:128249600-128297600	Weak transcription	HUVEC	blood vessel
7	chr7:128249600-128308400	Weak transcription	HSMM	muscle
8	chr7:128249600-128312200	Weak transcription	Psoas Muscle	Psoas
9	chr7:128249600-128319600	Weak transcription	NHLF	lung
10	chr7:128260000-128296400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:128260400-128300600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr7:128262200-128293200	Weak transcription	Brain Germinal Matrix	brain
13	chr7:128266400-128290400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr7:128272200-128300000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:128272400-128290400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:128272400-128290400	Weak transcription	K562	blood
17	chr7:128272400-128292400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr7:128272400-128293200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr7:128273600-128290600	Weak transcription	Fetal Brain Female	brain
20	chr7:128273800-128291800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr7:128274200-128296400	Weak transcription	Colonic Mucosa	Colon
22	chr7:128274600-128291200	Weak transcription	Esophagus	oesophagus
23	chr7:128275600-128295000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:128275800-128289600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:128279600-128296200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:128279800-128291200	Weak transcription	Gastric	stomach
27	chr7:128279800-128291800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr7:128279800-128292600	Weak transcription	Aorta	Aorta
29	chr7:128279800-128292600	Weak transcription	Brain Substantia Nigra	brain
30	chr7:128279800-128293000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr7:128279800-128293600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr7:128279800-128296400	Weak transcription	Brain Angular Gyrus	brain
33	chr7:128279800-128300000	Weak transcription	Dnd41	blood
34	chr7:128279800-128301400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr7:128280400-128291000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr7:128280400-128291800	Weak transcription	Right Ventricle	heart
37	chr7:128281200-128293200	Weak transcription	Ovary	ovary
38	chr7:128281400-128291200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr7:128281400-128291800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr7:128281400-128292400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr7:128281600-128290600	Weak transcription	Pancreas	Pancrea
42	chr7:128281600-128290800	Weak transcription	Brain Anterior Caudate	brain
43	chr7:128281600-128291800	Weak transcription	Brain Hippocampus Middle	brain
44	chr7:128281800-128291400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr7:128282200-128291400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr7:128282400-128295400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr7:128282400-128301400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr7:128282400-128312400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr7:128282600-128300000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr7:128282800-128291000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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