Variant report

Variant	rs2733246
Chromosome Location	chr15:45924981-45924982
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:45923721..45925487-chr15:45925745..45928411,3	MCF-7	breast:
2	chr15:45877501..45879866-chr15:45923125..45926614,3	MCF-7	breast:
3	chr15:45859095..45860936-chr15:45923807..45926477,2	K562	blood:

Variant related genes	Relation type
ENSG00000104164	Chromatin interaction
ENSG00000260170	Chromatin interaction
ENSG00000137767	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11632553	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11637892	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11637946	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11637984	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12440208	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs187095	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3985920	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs625047	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493164	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs66808613	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8039784	0.85[AMR][1000 genomes];0.85[EUR][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	nsv904188	chr15:45801035-45941689	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv904190	chr15:45892672-45960897	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	n/a
4	nsv904191	chr15:45902779-46381874	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2733246	SQRDL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45909600-45926600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:45923000-45925400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:45923800-45926600	Weak transcription	Right Ventricle	heart
4	chr15:45924000-45926400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:45924000-45926400	Weak transcription	Fetal Intestine Large	intestine
6	chr15:45924000-45926600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr15:45924000-45926600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:45924000-45926600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr15:45924000-45926600	Weak transcription	Brain Hippocampus Middle	brain
10	chr15:45924000-45926600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:45924000-45926600	Weak transcription	Stomach Mucosa	stomach
12	chr15:45924000-45926600	Weak transcription	Spleen	Spleen
13	chr15:45924000-45926800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:45924200-45925000	Enhancers	HMEC	breast
15	chr15:45924200-45926400	Weak transcription	Fetal Intestine Small	intestine
16	chr15:45924200-45926400	Weak transcription	A549	lung
17	chr15:45924200-45926600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:45924200-45926600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:45924200-45926600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:45924200-45926600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:45924200-45926600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:45924200-45926600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr15:45924200-45926600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:45924200-45926600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:45924200-45926600	Weak transcription	Adipose Nuclei	Adipose
26	chr15:45924200-45926600	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:45924200-45926600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr15:45924200-45926600	Weak transcription	Gastric	stomach
29	chr15:45924200-45926600	Weak transcription	Lung	lung
30	chr15:45924200-45926600	Weak transcription	Psoas Muscle	Psoas
31	chr15:45924200-45926600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr15:45924200-45926600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr15:45924200-45926600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr15:45924200-45926600	Weak transcription	GM12878-XiMat	blood
35	chr15:45924200-45926600	Weak transcription	HSMM	muscle
36	chr15:45924200-45926600	Weak transcription	HUVEC	blood vessel
37	chr15:45924200-45926600	Weak transcription	NH-A	brain
38	chr15:45924200-45926600	Weak transcription	NHLF	lung
39	chr15:45924200-45926800	Weak transcription	Fetal Kidney	kidney
40	chr15:45924400-45925000	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr15:45924400-45925000	Enhancers	NHEK	skin
42	chr15:45924400-45925200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:45924400-45925200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:45924400-45925400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:45924400-45925400	Enhancers	NHDF-Ad	bronchial
46	chr15:45924400-45926000	Weak transcription	Hela-S3	cervix
47	chr15:45924400-45926600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:45924400-45926600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr15:45924400-45926600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr15:45924400-45926600	Weak transcription	HSMMtube	muscle

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