Variant report

Variant	rs1421927
Chromosome Location	chr5:52242033-52242034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52239227..52240957-chr5:52240958..52243466,2	MCF-7	breast:
2	chr5:52240942..52242706-chr5:52367816..52370164,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10073432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1047481	0.86[CHB][hapmap]
rs1047483	0.83[CHB][hapmap]
rs10940281	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1363189	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1421928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2193968	0.83[CHB][hapmap]
rs2406371	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3088365	0.83[CHB][hapmap]
rs60478034	0.88[AFR][1000 genomes]
rs6888620	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6890588	0.83[CHB][hapmap]
rs6895049	0.83[CHB][hapmap]
rs7702592	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv830295	chr5:52084532-52257696	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	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
6	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
7	esv1794366	chr5:52240421-52249476	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1421927	ITGA1	cis	Thyroid	GTEx
rs1421927	ITGA2	cis	multi-tissue	Pritchard
rs1421927	ESM1	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52202200-52252200	Weak transcription	Small Intestine	intestine
2	chr5:52211600-52244400	Weak transcription	HepG2	liver
3	chr5:52218600-52242200	Weak transcription	Fetal Kidney	kidney
4	chr5:52220000-52243000	Weak transcription	Gastric	stomach
5	chr5:52220600-52252000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:52221400-52251800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:52224200-52244600	Weak transcription	Primary T cells from cord blood	blood
8	chr5:52229000-52246600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr5:52231600-52245400	Weak transcription	Colonic Mucosa	Colon
10	chr5:52232800-52249800	Weak transcription	Left Ventricle	heart
11	chr5:52235400-52243200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:52238800-52252200	Strong transcription	Liver	Liver
13	chr5:52240000-52245400	Weak transcription	Placenta	Placenta
14	chr5:52240000-52249800	Weak transcription	Aorta	Aorta
15	chr5:52240000-52253000	Weak transcription	Right Ventricle	heart
16	chr5:52240000-52253400	Weak transcription	Esophagus	oesophagus
17	chr5:52240000-52253600	Weak transcription	Lung	lung
18	chr5:52240200-52244200	Weak transcription	Fetal Lung	lung
19	chr5:52240200-52244200	Weak transcription	Fetal Stomach	stomach
20	chr5:52240200-52247000	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:52240200-52251800	Weak transcription	Fetal Intestine Small	intestine
22	chr5:52240200-52253400	Weak transcription	Spleen	Spleen
23	chr5:52240400-52251800	Weak transcription	Fetal Intestine Large	intestine
24	chr5:52240600-52242200	Active TSS	HMEC	breast
25	chr5:52240600-52244200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr5:52240800-52242400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:52240800-52242400	Enhancers	Hela-S3	cervix
28	chr5:52240800-52242400	Active TSS	NHLF	lung
29	chr5:52241200-52242200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:52241200-52242200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr5:52241200-52243200	Weak transcription	HSMM	muscle
32	chr5:52241200-52243200	Weak transcription	NH-A	brain
33	chr5:52241200-52243400	Enhancers	Rectal Smooth Muscle	rectum
34	chr5:52241200-52243600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:52241200-52243600	Weak transcription	Dnd41	blood
36	chr5:52241200-52245600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr5:52241200-52252000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr5:52241400-52242200	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr5:52241400-52242200	Enhancers	Colon Smooth Muscle	Colon
40	chr5:52241400-52242200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr5:52241400-52242400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:52241400-52243400	Weak transcription	Osteobl	bone
43	chr5:52241400-52244200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr5:52241400-52245000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr5:52241400-52245400	Enhancers	NHDF-Ad	bronchial
46	chr5:52241400-52247600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr5:52241600-52242200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr5:52241600-52242400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr5:52241600-52242800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:52241600-52243400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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