Variant report

Variant	rs2297380
Chromosome Location	chr15:41819322-41819323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41811420..41814118-chr15:41817482..41820204,2	K562	blood:

Variant related genes	Relation type
ENSG00000103932	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11070334	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11632399	0.85[EUR][1000 genomes]
rs11853341	0.84[ASN][1000 genomes]
rs11855860	0.84[ASN][1000 genomes]
rs1200345	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs1200346	0.85[EUR][1000 genomes]
rs1200348	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs1200349	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs12903050	0.81[AMR][1000 genomes]
rs2274858	0.85[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs2297378	0.84[EUR][1000 genomes]
rs2297381	0.82[ASW][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.82[YRI][hapmap]
rs2412615	0.94[ASN][1000 genomes]
rs28860492	0.84[EUR][1000 genomes]
rs3743031	0.80[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.93[ASN][1000 genomes]
rs7167667	0.83[GIH][hapmap]
rs7178957	0.83[EUR][1000 genomes]
rs721772	0.81[GIH][hapmap];0.83[MEX][hapmap]
rs932959	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][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	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv471241	chr15:41783814-41820200	Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv904112	chr15:41806658-41836234	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv569234	chr15:41815649-41822302	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2297380	RPAP1	cis	Artery Tibial	GTEx
rs2297380	TYRO3	cis	lung	GTEx
rs2297380	SPTBN5	cis	parietal	SCAN
rs2297380	RPAP1	cis	parietal	SCAN
rs2297380	LTK	cis	lung	GTEx
rs2297380	SPTBN5	cis	cerebellum	SCAN
rs2297380	RPAP1	cis	Adipose Subcutaneous	GTEx
rs2297380	RPAP1	cis	lymphoblastoid	seeQTL
rs2297380	RPAP1	cis	Esophagus Muscularis	GTEx
rs2297380	CAPN3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41806200-41820400	Weak transcription	HSMM	muscle
2	chr15:41806200-41822600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:41806400-41835200	Weak transcription	Right Atrium	heart
4	chr15:41806600-41824600	Weak transcription	Fetal Kidney	kidney
5	chr15:41806600-41835200	Weak transcription	Fetal Heart	heart
6	chr15:41806800-41822400	Weak transcription	NH-A	brain
7	chr15:41807200-41819400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:41807200-41835600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:41808000-41829600	Strong transcription	Fetal Stomach	stomach
10	chr15:41808200-41820600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:41808600-41823000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:41808600-41829200	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr15:41808600-41829600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:41808600-41835400	Weak transcription	Fetal Brain Male	brain
15	chr15:41808800-41829600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:41809000-41829400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:41809000-41829400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:41809600-41829200	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr15:41809600-41829400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:41810000-41820400	Weak transcription	Small Intestine	intestine
21	chr15:41810400-41819400	Weak transcription	Psoas Muscle	Psoas
22	chr15:41811600-41829600	Strong transcription	Fetal Intestine Large	intestine
23	chr15:41811600-41829800	Strong transcription	Fetal Muscle Leg	muscle
24	chr15:41811800-41829400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:41811800-41829400	Strong transcription	Brain Hippocampus Middle	brain
26	chr15:41811800-41829400	Strong transcription	Stomach Smooth Muscle	stomach
27	chr15:41811800-41829600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:41811800-41829600	Strong transcription	Brain Anterior Caudate	brain
29	chr15:41812000-41822800	Strong transcription	Placenta	Placenta
30	chr15:41812000-41823200	Strong transcription	Adipose Nuclei	Adipose
31	chr15:41812000-41829600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr15:41812200-41822800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr15:41812200-41823200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr15:41812200-41828800	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr15:41812200-41829200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr15:41812200-41829600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:41812200-41829600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:41812400-41823200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr15:41812400-41823200	Strong transcription	Lung	lung
40	chr15:41812400-41823600	Strong transcription	Gastric	stomach
41	chr15:41812400-41823800	Strong transcription	Fetal Brain Female	brain
42	chr15:41812400-41829200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:41812400-41829400	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr15:41812400-41829400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:41812400-41829400	Strong transcription	Liver	Liver
46	chr15:41812400-41829400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr15:41812400-41829400	Strong transcription	Fetal Intestine Small	intestine
48	chr15:41812400-41829400	Strong transcription	Left Ventricle	heart
49	chr15:41812400-41829600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr15:41812600-41823200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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