Variant report

Variant	rs1421941
Chromosome Location	chr5:52297951-52297952
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	chr5:52283580..52285693-chr5:52296693..52299370,2	MCF-7	breast:
2	chr5:52287570..52290507-chr5:52297245..52299058,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164171	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10042752	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10058636	0.91[ASN][1000 genomes]
rs10065796	1.00[JPT][hapmap]
rs10071255	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10071580	0.97[ASN][1000 genomes]
rs10073544	1.00[JPT][hapmap]
rs11948978	0.97[ASN][1000 genomes]
rs12523395	0.90[ASW][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes]
rs16880636	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1862639	0.85[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.97[ASN][1000 genomes]
rs3212386	0.80[CEU][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs3212402	0.97[ASN][1000 genomes]
rs3212412	0.97[ASN][1000 genomes]
rs3212417	0.97[ASN][1000 genomes]
rs3212627	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs55783963	0.97[ASN][1000 genomes]
rs66789666	0.90[AFR][1000 genomes]
rs67217308	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs67835512	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6883028	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7722066	0.87[YRI][hapmap]
rs9292002	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9292003	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	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
6	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1421941	DHX29	cis	parietal	SCAN
rs1421941	IL6ST	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52286200-52300400	Weak transcription	Gastric	stomach
2	chr5:52286200-52303400	Weak transcription	Small Intestine	intestine
3	chr5:52286200-52313600	Weak transcription	Lung	lung
4	chr5:52286600-52300000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:52286600-52302400	Weak transcription	Fetal Stomach	stomach
6	chr5:52286800-52298800	Weak transcription	Fetal Intestine Large	intestine
7	chr5:52287000-52299400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:52289200-52311600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:52290000-52299800	Weak transcription	NH-A	brain
10	chr5:52292400-52299200	Weak transcription	Esophagus	oesophagus
11	chr5:52292400-52301000	Weak transcription	Spleen	Spleen
12	chr5:52292400-52303200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:52293600-52304000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:52293800-52298800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:52293800-52299200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr5:52293800-52313400	Weak transcription	Fetal Intestine Small	intestine
17	chr5:52294200-52301200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:52294600-52302400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:52294600-52302600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr5:52294600-52302800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:52295600-52299000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:52295600-52299800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:52295800-52298800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:52295800-52300200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:52295800-52303000	Weak transcription	Brain Anterior Caudate	brain
26	chr5:52296000-52300200	Weak transcription	Osteobl	bone
27	chr5:52296200-52299000	Weak transcription	HMEC	breast
28	chr5:52296400-52299800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:52296600-52299000	Weak transcription	A549	lung
30	chr5:52297200-52299000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:52297400-52298400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:52297400-52299800	Weak transcription	Brain Hippocampus Middle	brain
33	chr5:52297600-52298200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:52297600-52298400	Weak transcription	NHEK	skin
35	chr5:52297600-52298800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:52297600-52299000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:52297600-52299000	Enhancers	HUVEC	blood vessel
38	chr5:52297600-52299800	Weak transcription	NHDF-Ad	bronchial
39	chr5:52297600-52300200	Weak transcription	NHLF	lung
40	chr5:52297600-52301000	Strong transcription	Hela-S3	cervix
41	chr5:52297600-52301600	Weak transcription	Brain Angular Gyrus	brain
42	chr5:52297600-52301600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr5:52297800-52299000	Enhancers	HepG2	liver
44	chr5:52297800-52299800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr5:52297800-52301600	Weak transcription	Brain Substantia Nigra	brain

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