Variant report

Variant	rs7643689
Chromosome Location	chr3:141475688-141475689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141462837..141465084-chr3:141474852..141476857,2	K562	blood:

Variant related genes	Relation type
ENSG00000114125	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	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533501	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16851689	1.00[JPT][hapmap]
rs16851691	1.00[JPT][hapmap]
rs16851704	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs16851717	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs16851740	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs16851752	0.83[EUR][1000 genomes]
rs17787772	0.82[JPT][hapmap]
rs1879284	0.85[EUR][1000 genomes]
rs1879285	0.85[EUR][1000 genomes]
rs1980192	0.85[EUR][1000 genomes]
rs2677426	0.82[JPT][hapmap]
rs3773840	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4538350	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4586785	1.00[JPT][hapmap]
rs4588340	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57983026	0.85[EUR][1000 genomes]
rs58115387	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58300294	0.83[EUR][1000 genomes]
rs59998648	0.81[AFR][1000 genomes]
rs60317930	0.86[EUR][1000 genomes]
rs60938827	0.83[EUR][1000 genomes]
rs61632965	0.81[AFR][1000 genomes]
rs6783647	0.85[EUR][1000 genomes]
rs6783736	0.85[EUR][1000 genomes]
rs6787712	0.84[EUR][1000 genomes]
rs72982481	0.83[EUR][1000 genomes]
rs73000336	0.83[EUR][1000 genomes]
rs7632069	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7642922	0.85[EUR][1000 genomes]
rs9789959	0.85[EUR][1000 genomes]
rs9789973	0.85[EUR][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	esv3349560	chr3:141475312-141479210	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7643689	RNF7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141461800-141498200	Weak transcription	Right Ventricle	heart
2	chr3:141465000-141481400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:141466200-141475800	Weak transcription	Psoas Muscle	Psoas
4	chr3:141467000-141477000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:141467000-141481600	Weak transcription	Lung	lung
6	chr3:141467000-141483400	Weak transcription	Fetal Lung	lung
7	chr3:141467200-141475800	Weak transcription	Primary T cells from cord blood	blood
8	chr3:141467400-141476000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:141470000-141481400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:141470000-141481600	Weak transcription	Placenta	Placenta
11	chr3:141470000-141482600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:141470000-141483400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:141470000-141483400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:141470000-141483400	Weak transcription	Fetal Stomach	stomach
15	chr3:141470000-141483600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:141470000-141486400	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:141470400-141482200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:141470800-141483400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:141471600-141483600	Weak transcription	Fetal Thymus	thymus
20	chr3:141471800-141483600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr3:141472000-141500800	Weak transcription	Thymus	Thymus
22	chr3:141472600-141484800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:141475600-141475800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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