Variant report

Variant	rs4390538
Chromosome Location	chr15:49289146-49289147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49287770..49290025-chr15:49461376..49464212,2	K562	blood:
2	chr15:49287788..49289553-chr15:49304281..49306822,2	K562	blood:

Variant related genes	Relation type
ENSG00000138593	Chromatin interaction
ENSG00000156958	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1054307	0.85[CHB][hapmap]
rs11070677	0.80[YRI][hapmap]
rs11070679	0.80[YRI][hapmap]
rs11542124	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11855740	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs11858917	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12904344	0.87[CEU][hapmap];0.80[JPT][hapmap]
rs16962017	0.92[CEU][hapmap];0.84[MEX][hapmap]
rs2305195	0.80[YRI][hapmap]
rs4284578	0.84[CHB][hapmap]
rs4435198	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775792	0.82[ASN][1000 genomes]
rs4775793	0.82[TSI][hapmap]
rs4775795	0.85[CHB][hapmap]
rs4775797	0.82[ASW][hapmap];0.84[YRI][hapmap]
rs7166261	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7167402	0.85[CHB][hapmap]
rs7183756	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8029751	0.94[ASW][hapmap];0.96[CEU][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8033060	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9920913	0.82[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4390538	CATSPER2P1	cis	cerebellum	SCAN
rs4390538	SPATA5L1	cis	parietal	SCAN
rs4390538	GALK2	cis	lymphoblastoid	seeQTL
rs4390538	MAP1A	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49268800-49309200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:49277400-49299400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:49280000-49293400	Strong transcription	Adipose Nuclei	Adipose
4	chr15:49280000-49294200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:49280200-49289200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:49280400-49293200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:49280400-49294400	Strong transcription	Placenta	Placenta
8	chr15:49280600-49291200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr15:49281200-49292800	Strong transcription	NHLF	lung
10	chr15:49281600-49293200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:49281600-49293400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:49281600-49293600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr15:49281600-49293800	Strong transcription	Primary hematopoietic stem cells	blood
14	chr15:49281800-49293000	Strong transcription	Liver	Liver
15	chr15:49282000-49293400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr15:49282000-49294000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:49282200-49293200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:49282200-49293400	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:49282200-49294800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:49282200-49294800	Strong transcription	Primary B cells from cord blood	blood
21	chr15:49282200-49294800	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:49282400-49289200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:49282400-49293200	Strong transcription	Fetal Intestine Large	intestine
24	chr15:49282600-49292200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr15:49282600-49293200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:49282600-49293200	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr15:49282600-49293200	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr15:49282600-49293400	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr15:49282800-49293200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr15:49282800-49293400	Strong transcription	Fetal Muscle Leg	muscle
31	chr15:49282800-49333400	Weak transcription	A549	lung
32	chr15:49283200-49293000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr15:49283200-49293200	Strong transcription	Fetal Lung	lung
34	chr15:49283200-49294800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr15:49283400-49289400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr15:49283400-49289400	Strong transcription	Lung	lung
37	chr15:49283400-49290000	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr15:49283400-49290000	Strong transcription	Stomach Smooth Muscle	stomach
39	chr15:49283400-49292800	Strong transcription	Duodenum Mucosa	Duodenum
40	chr15:49283400-49293000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr15:49283400-49293200	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:49283400-49293400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:49283600-49293200	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr15:49283600-49337600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr15:49283800-49293400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr15:49284200-49292400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr15:49284400-49289800	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr15:49284600-49293400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr15:49285000-49290600	Weak transcription	Spleen	Spleen
50	chr15:49285000-49291000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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