Variant report

Variant	rs10020652
Chromosome Location	chr4:110415750-110415751
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110406792..110410897-chr4:110414033..110418121,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207988	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10003981	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10005225	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10008457	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10009463	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10011971	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10030694	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17040433	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17040466	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17040498	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28412073	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28460762	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28541279	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28595287	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28597954	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28663368	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28680423	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28723468	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28829974	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57705376	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6533431	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6533432	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6812917	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6834714	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6837083	1.00[EUR][1000 genomes]
rs6838597	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6840561	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6852062	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6854516	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72898791	1.00[EUR][1000 genomes]
rs7665738	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7667502	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7674196	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7677736	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7681265	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7685647	1.00[EUR][1000 genomes]
rs7697001	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997563	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv525385	chr4:110395146-110466413	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110378800-110415800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:110385600-110415800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:110385600-110415800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr4:110385600-110415800	Weak transcription	Esophagus	oesophagus
5	chr4:110385800-110415800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:110385800-110415800	Weak transcription	Colonic Mucosa	Colon
7	chr4:110386000-110415800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr4:110386200-110415800	Weak transcription	Lung	lung
9	chr4:110386200-110415800	Weak transcription	Spleen	Spleen
10	chr4:110386400-110415800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:110387000-110415800	Weak transcription	Fetal Brain Male	brain
12	chr4:110387000-110415800	Weak transcription	Fetal Brain Female	brain
13	chr4:110387000-110416400	Weak transcription	Right Ventricle	heart
14	chr4:110393000-110415800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:110393000-110415800	Weak transcription	Gastric	stomach
16	chr4:110393000-110415800	Weak transcription	Left Ventricle	heart
17	chr4:110393000-110415800	Weak transcription	Pancreas	Pancrea
18	chr4:110393000-110417400	Weak transcription	Psoas Muscle	Psoas
19	chr4:110393200-110415800	Weak transcription	Small Intestine	intestine
20	chr4:110393200-110422600	Weak transcription	Right Atrium	heart
21	chr4:110393800-110415800	Weak transcription	Aorta	Aorta
22	chr4:110393800-110415800	Weak transcription	HSMMtube	muscle
23	chr4:110393800-110469200	Weak transcription	Stomach Mucosa	stomach
24	chr4:110394400-110415800	Weak transcription	Brain Anterior Caudate	brain
25	chr4:110395200-110415800	Weak transcription	A549	lung
26	chr4:110395600-110415800	Weak transcription	Hela-S3	cervix
27	chr4:110396200-110415800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:110400200-110415800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr4:110400200-110455400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr4:110400600-110415800	Weak transcription	Colon Smooth Muscle	Colon
31	chr4:110402000-110425000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:110403200-110415800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:110403200-110415800	Weak transcription	Brain Germinal Matrix	brain
34	chr4:110403400-110415800	Weak transcription	Brain Angular Gyrus	brain
35	chr4:110403600-110415800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:110403600-110415800	Weak transcription	Fetal Kidney	kidney
37	chr4:110403800-110415800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr4:110405200-110415800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr4:110406600-110415800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr4:110408400-110423000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:110409400-110467800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr4:110411400-110464600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr4:110412200-110423600	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr4:110412400-110419000	Strong transcription	Fetal Muscle Leg	muscle
45	chr4:110412400-110419400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:110412400-110421600	Strong transcription	HSMM	muscle
47	chr4:110412400-110424000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:110412400-110425400	Strong transcription	Primary T cells from cord blood	blood
49	chr4:110412400-110430200	Strong transcription	Liver	Liver
50	chr4:110412400-110443000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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