Variant report

Variant	rs4252229
Chromosome Location	chr5:68662094-68662095
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:68661918-68662117	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:68659738-68662513	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:68637589..68639798-chr5:68660289..68662388,2	MCF-7	breast:
2	chr5:68626792..68633026-chr5:68660168..68667090,13	MCF-7	breast:
3	chr5:68644789..68648896-chr5:68660361..68665573,5	K562	blood:
4	chr5:68626462..68633259-chr5:68656360..68665608,14	MCF-7	breast:
5	chr5:68530945..68532461-chr5:68661059..68663307,2	K562	blood:

Variant related genes	Relation type
RAD17	TF binding region
ENSG00000215006	Chromatin interaction
ENSG00000271045	Chromatin interaction
ENSG00000134058	Chromatin interaction
ENSG00000183323	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs17236219	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17236380	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17236422	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17236450	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17236618	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17236639	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4252222	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4252226	1.00[EUR][1000 genomes]
rs55754329	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55764482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56112110	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56362385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57344277	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57402724	1.00[EUR][1000 genomes]
rs57714822	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58172827	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58381452	1.00[EUR][1000 genomes]
rs58742544	1.00[EUR][1000 genomes]
rs59233462	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59776629	1.00[EUR][1000 genomes]
rs59799008	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60644166	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61244656	1.00[EUR][1000 genomes]
rs61290150	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6861518	1.00[EUR][1000 genomes]
rs6876889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772384	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772537	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73772541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772542	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772544	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772550	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7725200	1.00[EUR][1000 genomes]
rs8192269	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv881767	chr5:68625786-68733698	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68639200-68663400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:68643000-68664400	Weak transcription	Colonic Mucosa	Colon
3	chr5:68643200-68663200	Weak transcription	Small Intestine	intestine
4	chr5:68643800-68663600	Weak transcription	Brain Angular Gyrus	brain
5	chr5:68645800-68663400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:68647400-68663400	Weak transcription	Fetal Brain Male	brain
7	chr5:68647400-68663800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:68648400-68663400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:68649200-68663600	Weak transcription	Brain Substantia Nigra	brain
10	chr5:68649400-68663400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:68651400-68663600	Weak transcription	Right Ventricle	heart
12	chr5:68651400-68664400	Weak transcription	Aorta	Aorta
13	chr5:68653200-68664600	Weak transcription	Esophagus	oesophagus
14	chr5:68654400-68663200	Strong transcription	Primary B cells from peripheral blood	blood
15	chr5:68654800-68663400	Strong transcription	Fetal Muscle Leg	muscle
16	chr5:68655600-68662400	Strong transcription	Primary T cells from cord blood	blood
17	chr5:68656000-68663400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr5:68656000-68663400	Strong transcription	Fetal Thymus	thymus
19	chr5:68657000-68663200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr5:68657800-68663200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:68657800-68663200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr5:68657800-68663400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:68657800-68663400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr5:68658000-68662200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr5:68658000-68662400	Strong transcription	HUVEC	blood vessel
26	chr5:68658000-68662400	Strong transcription	K562	blood
27	chr5:68658000-68662600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:68658000-68663000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:68658000-68663000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:68658000-68663000	Strong transcription	Liver	Liver
31	chr5:68658000-68663200	Strong transcription	Primary B cells from cord blood	blood
32	chr5:68658000-68663200	Strong transcription	Placenta	Placenta
33	chr5:68658000-68663400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:68658000-68663400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:68658000-68663400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr5:68658200-68662600	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr5:68658200-68662600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr5:68658200-68662600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:68658200-68663000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:68658200-68663000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr5:68658200-68663200	Strong transcription	Adipose Nuclei	Adipose
42	chr5:68658200-68663200	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr5:68658200-68663400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:68658200-68663400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:68658200-68663400	Strong transcription	Fetal Intestine Large	intestine
46	chr5:68658400-68663000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:68658400-68663000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:68658400-68663000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr5:68658400-68663200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr5:68658600-68662200	Strong transcription	HMEC	breast

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