Variant report

Variant	rs6493496
Chromosome Location	chr15:51628119-51628120
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:51627940..51629861-chr15:51655726..51658198,2	MCF-7	breast:
2	chr15:51627112..51628862-chr15:51677820..51680161,2	MCF-7	breast:
3	chr15:51626293..51628181-chr15:51632058..51634071,2	MCF-7	breast:
4	chr15:51625487..51629588-chr15:51633484..51637530,6	MCF-7	breast:
5	chr15:51627542..51630536-chr15:51666856..51669527,2	MCF-7	breast:
6	chr15:51622619..51625126-chr15:51626375..51628421,2	MCF-7	breast:
7	chr15:51626312..51628802-chr15:51628827..51630843,2	K562	blood:
8	chr15:51578756..51579683-chr15:51627850..51628798,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000137869	Chromatin interaction
ENSG00000186417	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12441073	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17704365	0.86[JPT][hapmap]
rs4533220	0.82[JPT][hapmap]
rs4774585	0.90[GIH][hapmap]
rs60766173	0.83[ASN][1000 genomes]
rs7163193	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7172765	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8025191	0.82[CEU][hapmap];0.90[GIH][hapmap]
rs8041933	0.82[CEU][hapmap];0.90[GIH][hapmap]
rs8043240	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv904215	chr15:51542193-51673125	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6493496	GLDN	cis	Artery Tibial	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51622800-51628400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr15:51623400-51628400	Enhancers	Adipose Nuclei	Adipose
3	chr15:51624800-51628600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:51624800-51630400	Enhancers	Stomach Smooth Muscle	stomach
5	chr15:51625400-51628800	Enhancers	Primary B cells from peripheral blood	blood
6	chr15:51625400-51628800	Enhancers	Aorta	Aorta
7	chr15:51625400-51628800	Enhancers	Left Ventricle	heart
8	chr15:51625400-51628800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr15:51625800-51628400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr15:51626000-51628600	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr15:51626200-51629800	Enhancers	Fetal Heart	heart
12	chr15:51626600-51628200	Enhancers	Primary B cells from cord blood	blood
13	chr15:51626600-51629800	Weak transcription	Pancreas	Pancrea
14	chr15:51627000-51628200	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:51627000-51628200	Flanking Active TSS	GM12878-XiMat	blood
16	chr15:51627200-51628200	Weak transcription	Fetal Brain Male	brain
17	chr15:51627200-51628200	Weak transcription	Fetal Muscle Leg	muscle
18	chr15:51627200-51632800	Weak transcription	Spleen	Spleen
19	chr15:51627400-51628200	Enhancers	HepG2	liver
20	chr15:51627600-51628600	Enhancers	Brain Anterior Caudate	brain
21	chr15:51627800-51628400	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr15:51627800-51628600	Flanking Active TSS	Placenta	Placenta
23	chr15:51627800-51630200	Enhancers	Colon Smooth Muscle	Colon
24	chr15:51627800-51630400	Enhancers	Right Ventricle	heart
25	chr15:51628000-51628200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:51628000-51628200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:51628000-51628200	Enhancers	Fetal Kidney	kidney
28	chr15:51628000-51628200	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr15:51628000-51628400	Enhancers	Brain Angular Gyrus	brain
30	chr15:51628000-51628600	Enhancers	Fetal Stomach	stomach
31	chr15:51628000-51628800	Enhancers	Right Atrium	heart
32	chr15:51628000-51628800	Enhancers	Skeletal Muscle Male	skeletal muscle

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