Variant report

Variant	rs5003740
Chromosome Location	chr9:117660601-117660602
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:117659568..117662536-chr9:117667322..117669249,2	K562	blood:
2	chr9:117660259..117663236-chr9:117664218..117666178,2	MCF-7	breast:
3	chr9:117652267..117654785-chr9:117659593..117661164,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1126711	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1322067	0.86[ASN][1000 genomes]
rs1407309	0.87[ASN][1000 genomes]
rs1555457	0.85[AFR][1000 genomes]
rs2181036	0.86[ASN][1000 genomes]
rs2295800	0.86[ASN][1000 genomes]
rs2418324	0.85[ASN][1000 genomes]
rs2974	0.86[ASN][1000 genomes]
rs3181200	0.86[ASN][1000 genomes]
rs3181201	0.86[ASN][1000 genomes]
rs3181202	0.86[ASN][1000 genomes]
rs3181374	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4979470	0.87[ASN][1000 genomes]
rs6478117	0.86[ASN][1000 genomes]
rs7030090	0.86[ASN][1000 genomes]
rs7032773	0.82[ASN][1000 genomes]
rs7858603	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831695	chr9:117567626-117726247	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv893767	chr9:117627569-117689838	Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5003740	SLC31A1	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117652600-117662000	Weak transcription	Gastric	stomach
2	chr9:117654400-117661000	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr9:117655200-117661800	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr9:117655400-117661400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr9:117655600-117664800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr9:117656200-117660800	Enhancers	Primary B cells from cord blood	blood
7	chr9:117656200-117663400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr9:117656400-117663600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr9:117656600-117660800	Enhancers	Primary T cells from cord blood	blood
10	chr9:117657200-117662800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr9:117657200-117663600	Weak transcription	HSMMtube	muscle
12	chr9:117657600-117661200	Weak transcription	Esophagus	oesophagus
13	chr9:117657600-117661800	Weak transcription	Stomach Mucosa	stomach
14	chr9:117657800-117660800	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr9:117657800-117661000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr9:117657800-117661800	Weak transcription	Fetal Muscle Leg	muscle
17	chr9:117657800-117661800	Weak transcription	Right Ventricle	heart
18	chr9:117657800-117663200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:117657800-117664600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:117657800-117665400	Enhancers	HUVEC	blood vessel
21	chr9:117657800-117669600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr9:117658000-117662200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:117658000-117663200	Weak transcription	HMEC	breast
24	chr9:117658000-117663600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr9:117658200-117661000	Weak transcription	Liver	Liver
26	chr9:117658200-117661200	Weak transcription	Spleen	Spleen
27	chr9:117658200-117661800	Weak transcription	Placenta	Placenta
28	chr9:117658200-117663600	Weak transcription	Hela-S3	cervix
29	chr9:117658200-117663600	Weak transcription	NHEK	skin
30	chr9:117658200-117664600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr9:117658400-117661000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr9:117658400-117661800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:117658400-117663400	Weak transcription	A549	lung
34	chr9:117658400-117665200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr9:117658400-117665800	Enhancers	NHDF-Ad	bronchial
36	chr9:117658400-117667400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr9:117658600-117661800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr9:117658600-117669200	Weak transcription	Fetal Stomach	stomach
39	chr9:117659200-117661000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr9:117659200-117661000	Enhancers	Primary T cells fromperipheralblood	blood
41	chr9:117659200-117663400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:117659400-117663000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr9:117659600-117662800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr9:117659600-117663200	Enhancers	Primary B cells from peripheral blood	blood
45	chr9:117659600-117665400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr9:117659800-117660800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:117659800-117660800	Enhancers	Thymus	Thymus
48	chr9:117659800-117662000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr9:117659800-117663400	Enhancers	Fetal Thymus	thymus
50	chr9:117660000-117660800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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