Variant report

Variant	rs41423247
Chromosome Location	chr5:142778575-142778576
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:142766873..142770437-chr5:142777323..142782250,4	K562	blood:
2	chr5:142586500..142588941-chr5:142776031..142778884,2	K562	blood:
3	chr5:142750047..142752469-chr5:142777279..142779161,2	K562	blood:
4	chr5:142597121..142599287-chr5:142776012..142778713,2	K562	blood:
5	chr5:142777158..142779623-chr5:142783296..142786191,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113580	Chromatin interaction
ENSG00000145819	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10041520	0.81[ASN][1000 genomes]
rs1438732	0.87[AFR][1000 genomes]
rs2918415	0.85[AFR][1000 genomes]
rs2918418	0.82[AFR][1000 genomes]
rs2918419	0.81[AFR][1000 genomes]
rs2963151	0.81[AFR][1000 genomes]
rs2963154	0.85[AFR][1000 genomes]
rs33382	0.85[AFR][1000 genomes]
rs6196	0.82[AFR][1000 genomes]
rs72801090	0.90[AFR][1000 genomes]
rs72801096	0.82[AFR][1000 genomes]
rs7716360	0.81[ASN][1000 genomes]
rs852978	0.83[AFR][1000 genomes]
rs860458	0.81[AFR][1000 genomes]
rs9324918	0.86[AFR][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	nsv1023976	chr5:142692062-142813664	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv882994	chr5:142770135-142791677	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142761200-142778600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr5:142764800-142779800	Weak transcription	Esophagus	oesophagus
3	chr5:142766200-142779800	Weak transcription	Fetal Intestine Small	intestine
4	chr5:142766600-142779200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr5:142767200-142779400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:142767200-142779400	Weak transcription	Stomach Mucosa	stomach
7	chr5:142769000-142779400	Weak transcription	Gastric	stomach
8	chr5:142771800-142779200	Weak transcription	Left Ventricle	heart
9	chr5:142772000-142779200	Active TSS	GM12878-XiMat	blood
10	chr5:142773800-142778800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr5:142774000-142778600	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr5:142774200-142779000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:142774200-142779200	Active TSS	HMEC	breast
14	chr5:142774400-142778800	Active TSS	NHLF	lung
15	chr5:142774400-142779200	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr5:142774400-142782600	Transcr. at gene 5' and 3'	Dnd41	blood
17	chr5:142774600-142778600	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr5:142774600-142779400	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr5:142774600-142779800	Active TSS	Psoas Muscle	Psoas
20	chr5:142774600-142779800	Active TSS	Hela-S3	cervix
21	chr5:142775000-142779800	Active TSS	Right Atrium	heart
22	chr5:142775200-142779200	Active TSS	Thymus	Thymus
23	chr5:142775200-142779400	Active TSS	Stomach Smooth Muscle	stomach
24	chr5:142775200-142779800	Active TSS	Brain Cingulate Gyrus	brain
25	chr5:142775400-142778600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:142775400-142779200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:142775400-142779200	Active TSS	Brain Anterior Caudate	brain
28	chr5:142775400-142779200	Active TSS	HSMMtube	muscle
29	chr5:142775400-142779600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr5:142775400-142779600	Weak transcription	Small Intestine	intestine
31	chr5:142775400-142785200	Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr5:142775400-142785600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:142775600-142779200	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr5:142775600-142780000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:142775600-142785400	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr5:142775600-142785600	Active TSS	Brain Angular Gyrus	brain
37	chr5:142775800-142778600	Active TSS	Brain Hippocampus Middle	brain
38	chr5:142775800-142779200	Active TSS	Osteobl	bone
39	chr5:142775800-142782000	Flanking Active TSS	HUVEC	blood vessel
40	chr5:142776000-142779800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:142776000-142785600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:142776200-142779200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr5:142776200-142779200	Active TSS	Fetal Muscle Leg	muscle
44	chr5:142776200-142785400	Active TSS	Brain Substantia Nigra	brain
45	chr5:142776400-142779200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:142776400-142779600	Active TSS	Placenta Amnion	Placenta Amnion
47	chr5:142776600-142778800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:142776600-142779000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr5:142777000-142778800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr5:142777000-142779000	Active TSS	NHEK	skin

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