Variant report

Variant	rs17641488
Chromosome Location	chr5:154203121-154203122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:154201707..154203325-chr5:154206299..154208485,2	K562	blood:
2	chr5:154185361..154188131-chr5:154201569..154203996,2	MCF-7	breast:
3	chr5:154200501..154205115-chr5:154206575..154209973,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263361	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10515726	1.00[CHB][hapmap]
rs11167702	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11948782	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116316	1.00[CHB][hapmap]
rs17560103	0.85[CEU][hapmap]
rs17562321	0.83[GIH][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs348735	1.00[CHB][hapmap]
rs34951340	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3867430	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs56226335	0.87[ASN][1000 genomes]
rs593637	1.00[CHB][hapmap]
rs6886571	0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17641488	TNFRSF1A	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154169200-154204200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
2	chr5:154169200-154204200	Strong transcription	Dnd41	blood
3	chr5:154169400-154204000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:154169400-154204200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:154169400-154204200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr5:154169400-154205800	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr5:154169600-154204200	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr5:154174000-154212200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:154174800-154204400	Strong transcription	Placenta	Placenta
10	chr5:154175200-154204400	Strong transcription	Osteobl	bone
11	chr5:154175200-154204600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:154178200-154204000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:154181000-154211600	Strong transcription	Brain Hippocampus Middle	brain
14	chr5:154181200-154204800	Strong transcription	Brain Cingulate Gyrus	brain
15	chr5:154182000-154211400	Strong transcription	Left Ventricle	heart
16	chr5:154187000-154211400	Strong transcription	Fetal Stomach	stomach
17	chr5:154187600-154204200	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:154187600-154204400	Strong transcription	Brain Germinal Matrix	brain
19	chr5:154189400-154206000	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:154189800-154204600	Strong transcription	Lung	lung
21	chr5:154190400-154204200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:154191600-154208600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:154191800-154206200	Strong transcription	Brain Anterior Caudate	brain
24	chr5:154191800-154211600	Strong transcription	Adipose Nuclei	Adipose
25	chr5:154192400-154204200	Strong transcription	Brain Substantia Nigra	brain
26	chr5:154193000-154211800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:154193800-154204200	Strong transcription	Fetal Thymus	thymus
28	chr5:154194000-154209400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:154195600-154204600	Strong transcription	A549	lung
30	chr5:154195600-154208000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:154195600-154214400	Weak transcription	Small Intestine	intestine
32	chr5:154196000-154203600	Strong transcription	Liver	Liver
33	chr5:154196000-154229200	Weak transcription	Psoas Muscle	Psoas
34	chr5:154196400-154214000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr5:154196600-154208000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr5:154196800-154207400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr5:154197000-154204200	Strong transcription	Brain Angular Gyrus	brain
38	chr5:154197400-154203600	Weak transcription	NH-A	brain
39	chr5:154197600-154203400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:154197600-154208400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr5:154197600-154214400	Weak transcription	HUVEC	blood vessel
42	chr5:154197800-154214400	Weak transcription	Hela-S3	cervix
43	chr5:154198200-154204400	Strong transcription	Ovary	ovary
44	chr5:154198400-154207200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:154198600-154204200	Strong transcription	Rectal Smooth Muscle	rectum
46	chr5:154198600-154204400	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:154198600-154205800	Strong transcription	Colon Smooth Muscle	Colon
48	chr5:154198600-154206400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr5:154198600-154211200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr5:154198600-154211400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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