Variant report

Variant	rs9990664
Chromosome Location	chr4:160211232-160211233
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:160209916..160212415-chr4:160214012..160217879,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000216089	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10017696	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11100215	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12499444	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507095	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13103075	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13145422	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13150322	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28562885	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4295222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6811571	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6816396	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6824247	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6824488	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6834008	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6835746	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6847780	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848217	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6848706	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7349689	0.96[AMR][1000 genomes];0.90[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	nsv830129	chr4:160061694-160270760	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv1022771	chr4:160188801-160324683	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9990664	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160149400-160216800	Weak transcription	Small Intestine	intestine
2	chr4:160173200-160217400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:160186800-160225400	Weak transcription	Primary B cells from cord blood	blood
4	chr4:160189400-160235200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:160193400-160240200	Weak transcription	Gastric	stomach
6	chr4:160194400-160235600	Weak transcription	Fetal Stomach	stomach
7	chr4:160194400-160236600	Weak transcription	Primary T cells from cord blood	blood
8	chr4:160195200-160225600	Weak transcription	Placenta	Placenta
9	chr4:160200600-160235600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:160201800-160217200	Weak transcription	GM12878-XiMat	blood
11	chr4:160203600-160216600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:160205200-160216600	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:160205400-160214800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:160205400-160218200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:160205400-160219000	Weak transcription	Fetal Intestine Small	intestine
16	chr4:160205600-160217600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:160205800-160211400	Weak transcription	Brain Anterior Caudate	brain
18	chr4:160205800-160212600	Weak transcription	Right Atrium	heart
19	chr4:160205800-160213200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:160205800-160213200	Weak transcription	Left Ventricle	heart
21	chr4:160205800-160236400	Weak transcription	Pancreas	Pancrea
22	chr4:160205800-160260600	Weak transcription	Aorta	Aorta
23	chr4:160206200-160212600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:160206200-160214600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:160206200-160215000	Weak transcription	Right Ventricle	heart
26	chr4:160206200-160229000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:160207600-160211600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:160207800-160217600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:160208000-160213400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:160209000-160212200	Enhancers	Fetal Heart	heart
31	chr4:160209600-160212800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:160209800-160211600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr4:160209800-160211800	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr4:160209800-160211800	Enhancers	NHLF	lung
35	chr4:160209800-160212800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:160209800-160217800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr4:160210000-160211400	Weak transcription	Brain Angular Gyrus	brain
38	chr4:160210000-160216800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:160210000-160217800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr4:160210000-160229200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr4:160210200-160212400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:160210200-160213600	Enhancers	Muscle Satellite Cultured Cells	--
43	chr4:160210200-160214800	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr4:160210200-160217200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:160210400-160212800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:160210400-160214800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr4:160210600-160212600	Enhancers	A549	lung
48	chr4:160210600-160225400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr4:160210600-160238000	Weak transcription	Adipose Nuclei	Adipose
50	chr4:160210800-160211400	Enhancers	HSMMtube	muscle

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