Variant report

Variant	rs2249115
Chromosome Location	chr21:37849239-37849240
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:37804649..37806977-chr21:37848671..37850557,2	K562	blood:
2	chr21:37801129..37804550-chr21:37848189..37852893,8	MCF-7	breast:
3	chr21:37848424..37851198-chr21:37861596..37863686,2	K562	blood:
4	chr21:37846674..37849601-chr21:37873414..37874939,2	MCF-7	breast:
5	chr21:37845772..37848149-chr21:37849075..37851018,2	K562	blood:
6	chr21:37836196..37840141-chr21:37845664..37849647,3	K562	blood:
7	chr21:37837705..37840261-chr21:37847726..37849454,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159261	Chromatin interaction
ENSG00000230479	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs13047783	0.87[ASN][1000 genomes]
rs170182	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs219759	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs219765	0.90[ASN][1000 genomes]
rs2633334	0.98[ASN][1000 genomes]
rs2845764	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2845766	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2845769	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[ASN][1000 genomes]
rs2850102	0.93[ASN][1000 genomes]
rs2850108	0.97[ASN][1000 genomes]
rs2850110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35599107	0.88[ASN][1000 genomes]
rs35857368	0.90[ASN][1000 genomes]
rs55666618	0.88[ASN][1000 genomes]
rs59059205	0.91[ASN][1000 genomes]
rs59285877	0.91[ASN][1000 genomes]
rs59724458	0.91[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	nsv834090	chr21:37812545-38009542	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv33286	chr21:37827016-37861556	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv587470	chr21:37834641-37872447	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2249115	CLDN14	cis	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:37838000-37850800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr21:37843400-37851000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr21:37844400-37850000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr21:37845000-37850000	Weak transcription	GM12878-XiMat	blood
5	chr21:37846600-37849400	Weak transcription	HUVEC	blood vessel
6	chr21:37847400-37849800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr21:37848400-37850400	Transcr. at gene 5' and 3'	Liver	Liver
8	chr21:37849000-37850600	Enhancers	A549	lung
9	chr21:37849000-37852600	Enhancers	Fetal Heart	heart
10	chr21:37849200-37849400	Enhancers	Right Atrium	heart
11	chr21:37849200-37849600	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr21:37849200-37849600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr21:37849200-37849800	Enhancers	Brain Cingulate Gyrus	brain
14	chr21:37849200-37850000	Enhancers	Brain Anterior Caudate	brain
15	chr21:37849200-37850000	Enhancers	Brain Hippocampus Middle	brain
16	chr21:37849200-37850000	Enhancers	Placenta Amnion	Placenta Amnion
17	chr21:37849200-37850200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr21:37849200-37850600	Enhancers	Osteobl	bone
19	chr21:37849200-37850800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr21:37849200-37850800	Enhancers	NH-A	brain
21	chr21:37849200-37851000	Flanking Active TSS	HepG2	liver
22	chr21:37849200-37851400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr21:37849200-37852600	Enhancers	Stomach Mucosa	stomach

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