Variant report

Variant	rs1879285
Chromosome Location	chr3:141458723-141458724
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:29817431..29818176-chr3:141458193..141458736,2	Hela-S3	cervix:
2	chr3:141455674..141460093-chr3:141592801..141597430,19	MCF-7	breast:
3	chr3:141452499..141459593-chr3:141591792..141599045,17	MCF-7	breast:
4	chr3:141457377..141459578-chr3:141597906..141599752,2	MCF-7	breast:
5	chr3:141456676..141459122-chr3:141866884..141869547,2	MCF-7	breast:
6	chr3:141455466..141460652-chr3:141593125..141598625,15	K562	blood:
7	chr3:141378869..141381397-chr3:141457213..141459259,2	MCF-7	breast:
8	chr3:141457369..141459692-chr3:141539013..141541965,2	MCF-7	breast:
9	chr3:141455463..141459614-chr3:141593520..141599146,20	K562	blood:
10	chr3:141455584..141459326-chr3:141464266..141467931,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000069849	Chromatin interaction
ENSG00000114125	Chromatin interaction
ENSG00000114126	Chromatin interaction
ENSG00000103495	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11542226	0.85[EUR][1000 genomes]
rs1533501	0.80[EUR][1000 genomes]
rs16851704	0.88[EUR][1000 genomes]
rs16851717	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851740	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851752	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980192	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3773840	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4538350	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4588340	0.80[EUR][1000 genomes]
rs57394236	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57805567	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57983026	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58115387	0.85[EUR][1000 genomes]
rs58300294	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59998648	0.88[EUR][1000 genomes]
rs60938827	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61278509	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61294533	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61632965	0.88[EUR][1000 genomes]
rs6783647	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783736	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73872318	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73872319	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73872322	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73872326	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7632069	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642922	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643689	0.85[EUR][1000 genomes]
rs9789959	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9789973	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9790075	0.88[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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv877552	chr3:141420562-141466147	Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1879285	RNF7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141456600-141458800	Active TSS	Aorta	Aorta
2	chr3:141456600-141458800	Active TSS	Brain Angular Gyrus	brain
3	chr3:141456600-141458800	Active TSS	Fetal Intestine Small	intestine
4	chr3:141456600-141458800	Active TSS	Right Ventricle	heart
5	chr3:141456600-141458800	Active TSS	Stomach Smooth Muscle	stomach
6	chr3:141456600-141458800	Active TSS	NH-A	brain
7	chr3:141456600-141458800	Active TSS	NHDF-Ad	bronchial
8	chr3:141456600-141459000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:141456600-141459000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:141456600-141459000	Active TSS	Fetal Brain Female	brain
11	chr3:141456600-141459000	Active TSS	HSMM	muscle
12	chr3:141456600-141459200	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr3:141456600-141459200	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr3:141456600-141459200	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr3:141456600-141460000	Active TSS	Brain Hippocampus Middle	brain
16	chr3:141456800-141458800	Active TSS	Colonic Mucosa	Colon
17	chr3:141456800-141459200	Active TSS	GM12878-XiMat	blood
18	chr3:141456800-141459200	Active TSS	NHLF	lung
19	chr3:141457000-141458800	Active TSS	Lung	lung
20	chr3:141457400-141458800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:141457600-141458800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:141457600-141458800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:141457600-141459600	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr3:141457600-141460400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:141458000-141458800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:141458000-141459000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:141458000-141461400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:141458200-141458800	Flanking Active TSS	Colon Smooth Muscle	Colon
29	chr3:141458200-141458800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr3:141458200-141458800	Flanking Active TSS	HepG2	liver
31	chr3:141458200-141459000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:141458200-141459000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:141458200-141459000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:141458200-141459000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr3:141458200-141459000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:141458200-141459000	Enhancers	Placenta Amnion	Placenta Amnion
37	chr3:141458200-141459000	Flanking Active TSS	Hela-S3	cervix
38	chr3:141458200-141459000	Flanking Active TSS	Osteobl	bone
39	chr3:141458200-141459200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr3:141458200-141459200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:141458200-141459600	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr3:141458200-141459600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr3:141458200-141460000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr3:141458200-141460200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr3:141458200-141460200	Enhancers	Fetal Heart	heart
46	chr3:141458200-141461000	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr3:141458200-141470400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:141458400-141458800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:141458400-141458800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr3:141458400-141458800	Flanking Active TSS	Brain Anterior Caudate	brain

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