Variant report

Variant	rs2469204
Chromosome Location	chr15:77256130-77256131
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77254684..77256252-chr15:77267880..77270200,2	K562	blood:
2	chr15:77245562..77247184-chr15:77254642..77256229,2	K562	blood:
3	chr15:77254662..77256821-chr15:77261242..77263212,2	MCF-7	breast:
4	chr15:77237875..77240141-chr15:77253920..77256491,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243365	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12148386	0.85[ASN][1000 genomes]
rs12441484	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs12595586	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs17464903	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs2137307	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs4360890	0.88[CHB][hapmap]
rs4886503	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs4886507	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs4886829	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs66508953	0.86[ASN][1000 genomes]
rs7169663	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs7174673	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs8024737	0.86[ASN][1000 genomes]
rs8028294	0.89[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833058	chr15:77235895-77393640	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv517068	chr15:77254544-77381222	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2469204	SCAPER	cis	Esophagus Muscularis	GTEx
rs2469204	SCAPER	cis	Artery Tibial	GTEx
rs2469204	SCAPER	cis	lung	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77225000-77260200	Weak transcription	Right Ventricle	heart
2	chr15:77243800-77256200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr15:77244000-77256800	Weak transcription	Primary T cells from cord blood	blood
4	chr15:77247600-77256200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:77252000-77259000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:77252000-77259600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:77253600-77256800	Enhancers	Rectal Smooth Muscle	rectum
8	chr15:77254200-77259600	Weak transcription	Brain Anterior Caudate	brain
9	chr15:77254400-77256200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:77254400-77256200	Enhancers	Left Ventricle	heart
11	chr15:77254400-77256400	Enhancers	Psoas Muscle	Psoas
12	chr15:77254600-77256400	Enhancers	Aorta	Aorta
13	chr15:77254600-77259600	Weak transcription	Right Atrium	heart
14	chr15:77254600-77259800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr15:77255200-77259400	Weak transcription	Ovary	ovary
16	chr15:77255800-77256200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr15:77255800-77256400	Bivalent Enhancer	Fetal Intestine Small	intestine
18	chr15:77256000-77256200	Enhancers	H1 Cell Line	embryonic stem cell
19	chr15:77256000-77256200	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:77256000-77256200	Enhancers	Gastric	stomach
21	chr15:77256000-77256200	Enhancers	Pancreas	Pancrea
22	chr15:77256000-77256200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr15:77256000-77256200	Bivalent Enhancer	Stomach Mucosa	stomach
24	chr15:77256000-77256200	Bivalent Enhancer	HepG2	liver
25	chr15:77256000-77256400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:77256000-77256400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:77256000-77256400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr15:77256000-77256400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:77256000-77256400	Bivalent Enhancer	Fetal Muscle Leg	muscle
30	chr15:77256000-77256400	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr15:77256000-77256400	Enhancers	HSMM	muscle
32	chr15:77256000-77256600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:77256000-77256600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:77256000-77256600	Enhancers	Placenta Amnion	Placenta Amnion
35	chr15:77256000-77256800	Enhancers	Adipose Nuclei	Adipose
36	chr15:77256000-77257000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:77256000-77257000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:77256000-77257000	Enhancers	NH-A	brain
39	chr15:77256000-77257000	Enhancers	NHEK	skin
40	chr15:77256000-77257600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr15:77256000-77257800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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