Variant report

Variant	rs1900182
Chromosome Location	chr5:52388999-52389000
allele	A/C/G/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	chr5:52388996-52389633	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:52282305..52286125-chr5:52387011..52391029,5	MCF-7	breast:
2	chr5:52388236..52391143-chr5:52395060..52396954,3	K562	blood:
3	chr5:52388236..52391143-chr5:52394703..52396954,3	K562	blood:
4	chr5:52382323..52385100-chr5:52387808..52389930,2	K562	blood:

Variant related genes	Relation type
ENSG00000272123	TF binding region
ENSG00000249899	Chromatin interaction
ENSG00000164171	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10805445	0.84[ASN][1000 genomes]
rs10940291	0.84[ASN][1000 genomes]
rs1445941	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1445942	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17298242	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17298431	0.84[ASN][1000 genomes]
rs17298473	0.84[ASN][1000 genomes]
rs2075614	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2287950	0.83[AMR][1000 genomes]
rs2303124	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3212435	0.83[AMR][1000 genomes]
rs3212446	0.81[AMR][1000 genomes]
rs3212483	0.83[AMR][1000 genomes]
rs3212537	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs3212556	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3212603	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs3776788	0.83[AMR][1000 genomes]
rs3776789	0.83[AMR][1000 genomes]
rs3797500	0.83[AMR][1000 genomes]
rs62357234	0.83[AMR][1000 genomes]
rs62359377	0.84[ASN][1000 genomes]
rs62359378	0.84[ASN][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	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:52341200-52396400	Strong transcription	HMEC	breast
5	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:52343400-52392800	Weak transcription	Left Ventricle	heart
7	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas
8	chr5:52348600-52394800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:52352400-52389800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:52356800-52394000	Weak transcription	Fetal Kidney	kidney
11	chr5:52361200-52392800	Weak transcription	Small Intestine	intestine
12	chr5:52365800-52394800	Weak transcription	Right Ventricle	heart
13	chr5:52369000-52392800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:52370400-52394600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
16	chr5:52372000-52394800	Weak transcription	Colonic Mucosa	Colon
17	chr5:52372000-52394800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr5:52372200-52392800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:52372200-52394800	Weak transcription	Gastric	stomach
20	chr5:52372200-52394800	Weak transcription	Pancreas	Pancrea
21	chr5:52372400-52404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr5:52374200-52392800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr5:52378400-52405000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:52380000-52391200	Weak transcription	Fetal Brain Female	brain
25	chr5:52381200-52394200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:52382800-52395000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr5:52383000-52390800	Weak transcription	Fetal Heart	heart
28	chr5:52383000-52393000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr5:52383000-52394800	Weak transcription	Brain Anterior Caudate	brain
30	chr5:52383200-52394800	Weak transcription	Esophagus	oesophagus
31	chr5:52383200-52394800	Weak transcription	Spleen	Spleen
32	chr5:52383800-52389000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr5:52383800-52392200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr5:52383800-52392800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:52383800-52395000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:52384000-52394600	Weak transcription	Brain Angular Gyrus	brain
37	chr5:52384000-52394800	Weak transcription	Brain Substantia Nigra	brain
38	chr5:52384000-52395200	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:52384200-52394800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr5:52384400-52392800	Weak transcription	Fetal Intestine Small	intestine
41	chr5:52385200-52389800	Strong transcription	NHEK	skin
42	chr5:52385800-52392200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr5:52385800-52392400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr5:52385800-52394000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr5:52385800-52394600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr5:52385800-52395800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr5:52386000-52392600	Weak transcription	Primary T cells from cord blood	blood
48	chr5:52386000-52392800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr5:52386000-52392800	Weak transcription	Thymus	Thymus
50	chr5:52386200-52392400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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