Variant report

Variant	rs10039797
Chromosome Location	chr5:93968752-93968753
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	chr5:93966675..93969302-chr5:93973878..93976384,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10037940	0.89[EUR][1000 genomes]
rs10039102	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10052066	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10062402	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10072894	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10074178	0.82[AMR][1000 genomes]
rs10078522	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1031389	0.82[AMR][1000 genomes]
rs10476614	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1124667	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11948061	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12189060	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1451734	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1549179	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2112448	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2112449	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2112450	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs306574	0.82[EUR][1000 genomes]
rs306578	0.84[EUR][1000 genomes]
rs421521	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6556849	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs747880	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs755899	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs755901	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7709494	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7735924	0.80[EUR][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	esv2758002	chr5:93765205-94042201	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759354	chr5:93765205-94042201	Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv462254	chr5:93956937-94056825	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv598953	chr5:93956937-94056825	ZNF genes & repeats Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10039797	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs10039797	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93955000-93995400	Weak transcription	Gastric	stomach
2	chr5:93955400-93973000	Weak transcription	Ovary	ovary
3	chr5:93955400-93973000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:93955600-93972000	Weak transcription	Primary T cells from cord blood	blood
5	chr5:93955600-93974400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr5:93955600-93975200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:93955600-93975600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:93955600-93990800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr5:93955800-93969000	Weak transcription	Placenta	Placenta
10	chr5:93955800-93969400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:93955800-93973000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:93955800-93973200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:93955800-93974000	Weak transcription	HMEC	breast
14	chr5:93955800-93995400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:93955800-94027600	Weak transcription	NH-A	brain
16	chr5:93956000-93969600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:93956000-93972800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr5:93956000-93972800	Weak transcription	Thymus	Thymus
19	chr5:93956200-93969400	Weak transcription	NHEK	skin
20	chr5:93956200-93993200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr5:93957400-93972000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr5:93957400-93972800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:93957800-93982400	Weak transcription	Psoas Muscle	Psoas
24	chr5:93958800-93973000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr5:93959000-93972000	Weak transcription	NHDF-Ad	bronchial
26	chr5:93959000-93976400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr5:93960000-93972800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:93960200-93970400	Weak transcription	HUVEC	blood vessel
29	chr5:93962800-93975400	Weak transcription	NHLF	lung
30	chr5:93963200-93973200	Weak transcription	Esophagus	oesophagus
31	chr5:93963800-93995800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr5:93964400-93973600	Strong transcription	Hela-S3	cervix
33	chr5:93964600-93972400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr5:93964600-93995200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:93964800-93969000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:93964800-93969400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr5:93965200-93970200	Strong transcription	Dnd41	blood
38	chr5:93965400-93969200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:93965800-93970600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr5:93965800-93973600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr5:93965800-93988400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr5:93966000-93969000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr5:93966400-93971600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr5:93966400-93971800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:93966400-93972600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:93966600-93969200	Strong transcription	Primary hematopoietic stem cells	blood
47	chr5:93966600-93969400	Weak transcription	Brain Substantia Nigra	brain
48	chr5:93966600-93969600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr5:93966600-93969800	Weak transcription	Fetal Brain Male	brain
50	chr5:93966600-93971800	Weak transcription	Fetal Muscle Leg	muscle

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