Variant report

Variant	rs2409110
Chromosome Location	chr5:127433047-127433048
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:127425561..127430012-chr5:127430548..127434724,5	K562	blood:
2	chr5:127432707..127435327-chr5:127438169..127440618,3	K562	blood:
3	chr5:127419046..127421214-chr5:127431481..127433542,2	K562	blood:
4	chr5:127428694..127433227-chr5:127434862..127437524,4	K562	blood:
5	chr5:127432801..127435148-chr5:127441508..127443788,3	K562	blood:
6	chr5:127428726..127433227-chr5:127434885..127438247,5	K562	blood:
7	chr5:127429085..127432949-chr5:127432984..127436984,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000064651	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1112956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948128	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17764730	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1993878	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2250127	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2617617	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34576922	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3749748	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6860245	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6888037	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6889311	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734927	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs790154	0.94[CEU][hapmap];0.82[CHB][hapmap];0.84[AFR][1000 genomes]
rs790155	0.94[CEU][hapmap];0.82[CHB][hapmap];0.84[AFR][1000 genomes]
rs9327468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813981	chr5:127327649-127437401	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv4993	chr5:127405214-127445622	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv1825644	chr5:127427533-127450581	Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2409110	FLJ33630	Cis_1M	lymphoblastoid	RTeQTL
rs2409110	CTC-228N24.3	cis	Muscle Skeletal	GTEx
rs2409110	CTC-228N24.3	cis	Thyroid	GTEx
rs2409110	CTC-228N24.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127421400-127436400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:127421400-127450200	Weak transcription	Fetal Thymus	thymus
3	chr5:127421600-127466800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:127422000-127433200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:127422000-127434200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:127423000-127436600	Weak transcription	HSMMtube	muscle
7	chr5:127423600-127436400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:127423600-127444800	Weak transcription	Fetal Stomach	stomach
9	chr5:127423600-127494000	Weak transcription	K562	blood
10	chr5:127425800-127445000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr5:127426800-127433400	Weak transcription	Small Intestine	intestine
12	chr5:127429200-127436000	Weak transcription	Left Ventricle	heart
13	chr5:127429600-127436000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:127429800-127436000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:127430000-127441000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:127430200-127433600	Weak transcription	Psoas Muscle	Psoas
17	chr5:127430800-127433600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr5:127430800-127436000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:127431200-127434800	ZNF genes & repeats	A549	lung
20	chr5:127431400-127435600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:127431600-127435000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
22	chr5:127432200-127435200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:127432400-127454600	Weak transcription	Fetal Kidney	kidney
24	chr5:127432600-127437200	Weak transcription	NHDF-Ad	bronchial

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