Variant report

Variant	rs55641385
Chromosome Location	chr6:149971204-149971205
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr6:149968241-149971259	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:149884132..149889842-chr6:149966518..149971305,10	K562	blood:
2	chr6:149967293..149971613-chr6:150037790..150041524,8	K562	blood:
3	chr6:149865491..149867139-chr6:149970977..149973867,2	K562	blood:
4	chr6:149967309..149971944-chr6:150037502..150040952,6	MCF-7	breast:
5	chr6:149969487..149971965-chr6:150038903..150040820,3	K562	blood:
6	chr6:149884836..149889436-chr6:149966369..149971850,7	K562	blood:

No data

Variant related genes	Relation type
KATNA1	TF binding region
ENSG00000055211	Chromatin interaction
ENSG00000131023	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs56277480	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs56410385	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426124	1.00[AFR][1000 genomes]
rs62621196	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv289	chr6:149864898-149998818	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv5534	chr6:149864898-149998818	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv886762	chr6:149866452-150174507	Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1792620	chr6:149909491-150083621	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55641385	NUP43	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149970000-149978400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:149970000-149983800	Weak transcription	Gastric	stomach
3	chr6:149970000-149989600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:149970200-149972000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:149970200-149977600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:149970200-149977800	Weak transcription	HMEC	breast
7	chr6:149970200-149978200	Weak transcription	Left Ventricle	heart
8	chr6:149970200-149983000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:149970200-149985800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:149970200-149988200	Weak transcription	Aorta	Aorta
11	chr6:149970200-149989600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:149970200-149989600	Weak transcription	Small Intestine	intestine
13	chr6:149970200-149989800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:149970400-149972000	Weak transcription	Primary B cells from cord blood	blood
15	chr6:149970400-149976800	Weak transcription	Fetal Brain Female	brain
16	chr6:149970400-149977000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:149970400-149977000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:149970400-149977400	Weak transcription	Placenta	Placenta
19	chr6:149970400-149977600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:149970400-149977800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:149970400-149977800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:149970400-149977800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:149970400-149977800	Weak transcription	Liver	Liver
24	chr6:149970400-149977800	Weak transcription	Brain Angular Gyrus	brain
25	chr6:149970400-149977800	Weak transcription	Fetal Intestine Large	intestine
26	chr6:149970400-149977800	Weak transcription	Fetal Kidney	kidney
27	chr6:149970400-149977800	Weak transcription	HSMMtube	muscle
28	chr6:149970400-149978000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:149970400-149978000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:149970400-149978000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:149970400-149978000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:149970400-149978000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:149970400-149978000	Weak transcription	NH-A	brain
34	chr6:149970400-149978200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr6:149970400-149978200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr6:149970400-149978200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr6:149970400-149978200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:149970400-149978200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:149970400-149978200	Weak transcription	Thymus	Thymus
40	chr6:149970400-149978600	Weak transcription	Brain Germinal Matrix	brain
41	chr6:149970400-149981000	Weak transcription	HSMM	muscle
42	chr6:149970400-149981400	Weak transcription	NHEK	skin
43	chr6:149970400-149981400	Weak transcription	Osteobl	bone
44	chr6:149970400-149982200	Weak transcription	NHDF-Ad	bronchial
45	chr6:149970400-149982600	Weak transcription	HUVEC	blood vessel
46	chr6:149970400-149982800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr6:149970400-149982800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:149970400-149982800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr6:149970400-149982800	Weak transcription	NHLF	lung
50	chr6:149970400-149983000	Weak transcription	H1 Cell Line	embryonic stem cell

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