Variant report

Variant	rs10056685
Chromosome Location	chr5:93972257-93972258
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:93969932..93973613-chr5:93973766..93976891,3	K562	blood:
2	chr5:93953624..93955883-chr5:93971735..93973359,2	K562	blood:

Variant related genes	Relation type
ENSG00000270133	Chromatin interaction
ENSG00000185261	Chromatin interaction
ENSG00000133302	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10037228	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10041551	0.91[CEU][hapmap]
rs10044797	0.90[CEU][hapmap]
rs10051931	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10053484	0.91[CEU][hapmap]
rs10058130	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10058618	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs10070258	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10076188	0.91[CEU][hapmap]
rs10078304	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs10476612	0.91[CEU][hapmap]
rs10476613	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10476615	0.91[CEU][hapmap]
rs11741678	0.81[CHB][hapmap];0.86[ASN][1000 genomes]
rs11743258	0.86[ASN][1000 genomes]
rs11949227	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11955373	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs12516225	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12517866	0.91[CEU][hapmap]
rs12518034	0.91[CEU][hapmap]
rs12522312	0.91[CEU][hapmap]
rs13353994	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13354061	0.87[EUR][1000 genomes]
rs13358642	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs13361811	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13362556	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1376713	0.81[CHB][hapmap]
rs2101898	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs2305391	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs28645132	0.89[EUR][1000 genomes]
rs28787271	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs306573	0.91[CEU][hapmap]
rs306575	0.91[CEU][hapmap]
rs3756470	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs55974730	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6873364	0.86[CEU][hapmap]
rs6879307	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs755898	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7705424	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7725095	0.86[CEU][hapmap]
rs7725698	0.82[CEU][hapmap]
rs7737779	0.91[CEU][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10056685	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs10056685	ANKRD32	cis	multi-tissue	Pritchard
rs10056685	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

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	chr5:93955600-93974400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:93955600-93975200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr5:93955600-93975600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:93955600-93990800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:93955800-93973000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:93955800-93973200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:93955800-93974000	Weak transcription	HMEC	breast
11	chr5:93955800-93995400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:93955800-94027600	Weak transcription	NH-A	brain
13	chr5:93956000-93972800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr5:93956000-93972800	Weak transcription	Thymus	Thymus
15	chr5:93956200-93993200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr5:93957400-93972800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:93957800-93982400	Weak transcription	Psoas Muscle	Psoas
18	chr5:93958800-93973000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr5:93959000-93976400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr5:93960000-93972800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr5:93962800-93975400	Weak transcription	NHLF	lung
22	chr5:93963200-93973200	Weak transcription	Esophagus	oesophagus
23	chr5:93963800-93995800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:93964400-93973600	Strong transcription	Hela-S3	cervix
25	chr5:93964600-93972400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr5:93964600-93995200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:93965800-93973600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr5:93965800-93988400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:93966400-93972600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:93966600-93972800	Weak transcription	Brain Germinal Matrix	brain
31	chr5:93966600-93974800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:93966600-93980000	Weak transcription	Left Ventricle	heart
33	chr5:93966600-93990800	Weak transcription	Brain Hippocampus Middle	brain
34	chr5:93967200-93972400	Weak transcription	Adipose Nuclei	Adipose
35	chr5:93967200-93974400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:93967200-93979600	Weak transcription	Brain Anterior Caudate	brain
37	chr5:93967400-93972800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:93967400-93974400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:93967400-93974800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr5:93967400-93975200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:93967400-93975400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr5:93967400-93991400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr5:93967600-93979800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr5:93967600-93988200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr5:93967800-93973400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr5:93967800-93978200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:93967800-93991000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr5:93968000-93973000	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr5:93968000-93973400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:93968000-93974400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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