Variant report

Variant	rs17267540
Chromosome Location	chr1:211491130-211491131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210545971..210547559-chr1:211491010..211492840,2	MCF-7	breast:
2	chr1:211431679..211433826-chr1:211490845..211492829,2	K562	blood:
3	chr1:211461477..211464253-chr1:211490231..211493061,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RD3-6	chr1:211490796-211491142	NONHSAT009287

Variant related genes	Relation type
ENSG00000117625	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17017384	0.83[AFR][1000 genomes]
rs17017406	0.83[AFR][1000 genomes]
rs2230779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3125835	1.00[CHB][hapmap]
rs41303275	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41307648	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58393607	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6540679	0.87[CEU][hapmap];0.83[GIH][hapmap]
rs74138736	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17267540	CPA4	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211444800-211491200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:211461200-211499600	Weak transcription	Psoas Muscle	Psoas
3	chr1:211461400-211499600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:211461600-211499600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:211467200-211493800	Weak transcription	Fetal Brain Male	brain
6	chr1:211467800-211494200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:211474800-211497000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:211478600-211499800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:211479400-211492200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:211483600-211491200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:211483600-211499600	Weak transcription	Fetal Heart	heart
12	chr1:211484600-211491600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:211486400-211499400	Weak transcription	Stomach Mucosa	stomach
14	chr1:211486400-211500200	Weak transcription	Small Intestine	intestine
15	chr1:211487200-211491400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:211487200-211492200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:211487200-211492800	Weak transcription	HepG2	liver
18	chr1:211487200-211496600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:211487200-211497000	Weak transcription	Fetal Stomach	stomach
20	chr1:211487200-211498800	Weak transcription	Thymus	Thymus
21	chr1:211487200-211499400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:211487200-211499600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:211487200-211499600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:211487200-211499600	Weak transcription	Brain Angular Gyrus	brain
25	chr1:211487200-211499600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:211487200-211499600	Weak transcription	Fetal Intestine Small	intestine
27	chr1:211487200-211499600	Weak transcription	Gastric	stomach
28	chr1:211487200-211499600	Weak transcription	Left Ventricle	heart
29	chr1:211487200-211499600	Weak transcription	Lung	lung
30	chr1:211487200-211499600	Weak transcription	Pancreas	Pancrea
31	chr1:211487200-211499800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:211487200-211499800	Weak transcription	Aorta	Aorta
33	chr1:211487200-211499800	Weak transcription	Esophagus	oesophagus
34	chr1:211487200-211499800	Weak transcription	Ovary	ovary
35	chr1:211487200-211499800	Weak transcription	Right Ventricle	heart
36	chr1:211487200-211500200	Weak transcription	Spleen	Spleen
37	chr1:211487400-211491600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:211487400-211499600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:211487400-211499600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:211487400-211499600	Weak transcription	Brain Anterior Caudate	brain
41	chr1:211487400-211499600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:211487400-211499600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:211487400-211499800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:211487400-211499800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:211487400-211499800	Weak transcription	HSMMtube	muscle
46	chr1:211487600-211499600	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:211487600-211499600	Weak transcription	NHLF	lung
48	chr1:211488000-211499600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:211488000-211499600	Weak transcription	Brain Substantia Nigra	brain
50	chr1:211488200-211494200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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