Variant report

Variant	rs835135
Chromosome Location	chr5:14926603-14926604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14664017..14666090-chr5:14925708..14927348,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261360	Chromatin interaction
ENSG00000154124	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1811466	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1984447	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2591507	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2591510	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2592010	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2921611	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2921612	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2921613	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs728844	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835104	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs835105	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs835128	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs860665	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv830212	chr5:14784197-14966683	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	esv2755538	chr5:14814900-14927500	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv530221	chr5:14859687-15364470	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv432717	chr5:14887400-15126500	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1017579	chr5:14888997-15194335	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv597261	chr5:14913369-14962587	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv881238	chr5:14917813-14950952	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv881343	chr5:14917813-14956699	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv881445	chr5:14917813-14960920	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv881333	chr5:14924458-14962587	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs835135	SEC22B	trans	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14916600-14929200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:14924000-14929400	Weak transcription	Fetal Heart	heart
3	chr5:14924600-14927200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr5:14924800-14926800	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr5:14924800-14927200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:14924800-14927400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:14924800-14927400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:14925000-14927200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr5:14925200-14926800	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr5:14925200-14927200	Enhancers	HMEC	breast
11	chr5:14925200-14927400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:14925400-14926800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:14925400-14927000	Enhancers	HSMM	muscle
14	chr5:14925400-14927200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr5:14925400-14927200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:14925400-14927400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr5:14925400-14927400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:14925400-14927400	Enhancers	NHDF-Ad	bronchial
19	chr5:14925400-14931000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:14925600-14927400	Enhancers	Primary T cells fromperipheralblood	blood
21	chr5:14925800-14927000	Enhancers	NHLF	lung
22	chr5:14926000-14926800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr5:14926000-14927200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:14926000-14927200	Enhancers	Right Atrium	heart
25	chr5:14926000-14927400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:14926200-14927200	Enhancers	Primary T cells from cord blood	blood
27	chr5:14926200-14927200	Enhancers	Placenta	Placenta
28	chr5:14926400-14929200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:14926600-14926800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:14926600-14927000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr5:14926600-14927400	Enhancers	Muscle Satellite Cultured Cells	--
32	chr5:14926600-14927400	Enhancers	Dnd41	blood
33	chr5:14926600-14927400	Enhancers	Osteobl	bone
34	chr5:14926600-14927600	Weak transcription	Lung	lung
35	chr5:14926600-14927600	Enhancers	NH-A	brain
36	chr5:14926600-14929200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:14926600-14929400	Weak transcription	Left Ventricle	heart

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