Variant report

Variant	rs62375502
Chromosome Location	chr5:142707734-142707735
allele	C/T
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	chr5:142706560-142708655	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:142707616-142707925	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:142706358-142707926	GM12878	blood:	n/a	n/a
4	POLR2A	chr5:142706566-142707947	GM12892	blood:	n/a	n/a
5	POLR2A	chr5:142707209-142707865	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr5:142707109-142707911	GM12878	blood:	n/a	n/a
7	POLR2A	chr5:142706944-142708022	GM12892	blood:	n/a	n/a
8	POLR2A	chr5:142707700-142707875	GM12878	blood:	n/a	n/a
9	CBX3	chr5:142707390-142707808	K562	blood:	n/a	n/a
10	POLR2A	chr5:142707125-142708008	GM12892	blood:	n/a	n/a
11	POLR2A	chr5:142707697-142707876	K562	blood:	n/a	n/a

Variant related genes	Relation type
RPL7P21	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10482634	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10482655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10482682	1.00[ASN][1000 genomes]
rs11745958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11750172	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17209216	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17209237	0.92[EUR][1000 genomes]
rs17209251	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17209258	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17339455	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17399352	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2013935	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2398631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2963156	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33944801	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912903	1.00[ASN][1000 genomes]
rs4912906	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4912908	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4986593	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62375499	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324916	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	esv1825941	chr5:142568715-142728031	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1023976	chr5:142692062-142813664	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1033408	chr5:142701353-142738882	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142658400-142714800	Weak transcription	Esophagus	oesophagus
2	chr5:142692400-142710600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:142693200-142714400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr5:142693400-142721000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr5:142693800-142747400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr5:142696400-142708200	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:142697200-142714600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:142697200-142720400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:142697800-142711400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:142698200-142709200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:142699000-142720600	Weak transcription	Hela-S3	cervix
12	chr5:142699200-142721400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:142699600-142709400	Weak transcription	NHLF	lung
14	chr5:142699600-142711200	Weak transcription	NHDF-Ad	bronchial
15	chr5:142699600-142714400	Weak transcription	Osteobl	bone
16	chr5:142699600-142715800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr5:142699600-142718600	Weak transcription	Gastric	stomach
18	chr5:142699600-142720200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:142700200-142711200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:142701200-142714400	Weak transcription	Fetal Heart	heart
21	chr5:142701600-142708200	ZNF genes & repeats	GM12878-XiMat	blood
22	chr5:142702000-142725800	Weak transcription	Aorta	Aorta
23	chr5:142702400-142711200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr5:142703000-142709400	Weak transcription	Brain Anterior Caudate	brain
25	chr5:142703000-142711200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:142703000-142711200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr5:142703000-142727200	Weak transcription	HSMM	muscle
28	chr5:142703800-142718600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr5:142704000-142708200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:142704000-142708400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
31	chr5:142704000-142709400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:142704200-142709600	Weak transcription	Brain Substantia Nigra	brain
33	chr5:142704200-142728800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:142704400-142717400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:142704800-142708200	Weak transcription	Liver	Liver
36	chr5:142705200-142725600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr5:142705800-142722400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr5:142706400-142709000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr5:142706400-142710800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr5:142706600-142708000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:142706600-142708800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
42	chr5:142706600-142709200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr5:142706800-142708000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
44	chr5:142706800-142708000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr5:142706800-142708000	Enhancers	Left Ventricle	heart
46	chr5:142706800-142709200	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr5:142707000-142708000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:142707000-142708200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr5:142707000-142708600	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr5:142707000-142715800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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