Variant report

Variant	rs6880055
Chromosome Location	chr5:52389428-52389429
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

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
2	CTCF	chr5:52389280-52389430	HCPEpiC	choroid plexus:	n/a	n/a
3	POLR2A	chr5:52389090-52389519	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:52282305..52286125-chr5:52387011..52391029,5	MCF-7	breast:
2	chr5:52386358..52388185-chr5:52389009..52390618,2	MCF-7	breast:
3	chr5:52388236..52391143-chr5:52395060..52396954,3	K562	blood:
4	chr5:52388236..52391143-chr5:52394703..52396954,3	K562	blood:
5	chr5:52382323..52385100-chr5:52387808..52389930,2	K562	blood:

No data

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

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1062535	0.80[CEU][hapmap]
rs10940290	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1126643	0.87[YRI][hapmap]
rs11959632	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12515364	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12521915	0.91[CEU][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12657429	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12657501	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12657972	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12657980	0.83[ASN][1000 genomes]
rs1316250	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1363192	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1421937	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1445943	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs16880669	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2303122	0.91[CEU][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs3212424	0.82[CEU][hapmap]
rs3212438	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3212439	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3212441	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3212450	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3212453	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3212455	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3212457	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3212458	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3212461	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3212464	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3212478	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3212480	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3212481	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3212486	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3212600	0.83[AFR][1000 genomes]
rs3212601	0.83[AFR][1000 genomes]
rs3212619	0.80[EUR][1000 genomes]
rs3756537	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3776787	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3797495	0.83[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3797496	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3797498	0.83[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3822558	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3926397	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62357232	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62357233	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6898333	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7725246	0.84[CEU][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.80[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6880055	ITGA1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:100 , 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	chr5:52383800-52392200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr5:52383800-52392800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:52383800-52395000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:52384000-52394600	Weak transcription	Brain Angular Gyrus	brain
36	chr5:52384000-52394800	Weak transcription	Brain Substantia Nigra	brain
37	chr5:52384000-52395200	Weak transcription	Brain Hippocampus Middle	brain
38	chr5:52384200-52394800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr5:52384400-52392800	Weak transcription	Fetal Intestine Small	intestine
40	chr5:52385200-52389800	Strong transcription	NHEK	skin
41	chr5:52385800-52392200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr5:52385800-52392400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr5:52385800-52394000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr5:52385800-52394600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr5:52385800-52395800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr5:52386000-52392600	Weak transcription	Primary T cells from cord blood	blood
47	chr5:52386000-52392800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr5:52386000-52392800	Weak transcription	Thymus	Thymus
49	chr5:52386200-52392400	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr5:52386200-52394800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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