Variant report

Variant	rs56358931
Chromosome Location	chr3:141515877-141515878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141514623..141517093-chr3:141594365..141597102,3	K562	blood:
2	chr3:141512385..141514175-chr3:141514363..141516660,2	MCF-7	breast:
3	chr3:141509966..141511631-chr3:141513470..141515966,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs4234468	0.95[ASN][1000 genomes]
rs4234469	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4683409	0.83[ASN][1000 genomes]
rs6806847	0.96[ASN][1000 genomes]
rs6809291	0.89[EUR][1000 genomes]
rs9859089	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56358931	RNF7	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141512800-141516400	Enhancers	Primary hematopoietic stem cells	blood
2	chr3:141513200-141516000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr3:141513600-141517800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:141513800-141516200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:141513800-141516200	Enhancers	Esophagus	oesophagus
6	chr3:141513800-141517000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:141514000-141517800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:141514200-141516000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:141514200-141516000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:141514200-141516000	Enhancers	Placenta	Placenta
11	chr3:141514200-141516400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:141514200-141517200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:141514200-141517600	Flanking Active TSS	Dnd41	blood
14	chr3:141514600-141516000	Enhancers	K562	blood
15	chr3:141514600-141516200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:141514600-141517600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr3:141514800-141516000	Enhancers	Fetal Stomach	stomach
18	chr3:141514800-141516000	Flanking Active TSS	Thymus	Thymus
19	chr3:141514800-141517000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:141514800-141517800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:141515000-141516000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:141515000-141516000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:141515000-141516000	Enhancers	Brain Cingulate Gyrus	brain
24	chr3:141515000-141516000	Enhancers	Brain Substantia Nigra	brain
25	chr3:141515000-141516000	Enhancers	Fetal Intestine Small	intestine
26	chr3:141515000-141516000	Enhancers	Lung	lung
27	chr3:141515000-141516000	Enhancers	Spleen	Spleen
28	chr3:141515000-141516200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:141515000-141516200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr3:141515000-141517200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:141515000-141517600	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr3:141515000-141517800	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr3:141515200-141516000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:141515200-141516000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:141515200-141516000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:141515200-141516000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:141515200-141516000	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr3:141515200-141516000	Enhancers	Fetal Intestine Large	intestine
39	chr3:141515200-141516000	Enhancers	Left Ventricle	heart
40	chr3:141515200-141516200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:141515200-141516200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr3:141515200-141516400	Enhancers	Pancreas	Pancrea
43	chr3:141515200-141517000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:141515200-141517200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr3:141515200-141517200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr3:141515200-141517200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr3:141515200-141517200	Flanking Active TSS	HSMMtube	muscle
48	chr3:141515200-141517400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr3:141515200-141517400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:141515200-141517600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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