Variant report

Variant	rs13354061
Chromosome Location	chr5:93993015-93993016
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	chr5:93979164..93980988-chr5:93992577..93994431,2	MCF-7	breast:
2	chr5:93992680..93994968-chr5:93995971..93998470,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10035632	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10037228	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041262	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041551	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10041843	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10044797	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10051931	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10053484	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10056685	0.87[EUR][1000 genomes]
rs10058130	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10058618	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10061737	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10062248	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10070258	0.88[EUR][1000 genomes]
rs10076188	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10076461	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078049	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10078304	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10476612	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10476613	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10476615	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11949227	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11955373	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11960129	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12516225	0.88[EUR][1000 genomes]
rs12517866	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518034	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522312	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13169956	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13353994	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13358642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361811	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13362556	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28645132	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28787271	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs306573	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs306575	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4869218	0.90[EUR][1000 genomes]
rs55974730	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6862592	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873364	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6879307	0.88[EUR][1000 genomes]
rs755898	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7705424	0.88[EUR][1000 genomes]
rs7725095	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7725698	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7731360	0.81[EUR][1000 genomes]
rs7737779	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv882386	chr5:93973177-94008969	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13354061	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs13354061	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL
rs13354061	ANKRD32	cis	multi-tissue	Pritchard

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93955000-93995400	Weak transcription	Gastric	stomach
2	chr5:93955800-93995400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:93955800-94027600	Weak transcription	NH-A	brain
4	chr5:93956200-93993200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr5:93963800-93995800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:93964600-93995200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr5:93968000-93995200	Weak transcription	HSMM	muscle
8	chr5:93969400-94008400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:93971400-93995400	Weak transcription	Spleen	Spleen
10	chr5:93973800-93995200	Weak transcription	Lung	lung
11	chr5:93973800-94004200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr5:93974200-93995400	Weak transcription	Ovary	ovary
13	chr5:93974400-93995200	Weak transcription	Thymus	Thymus
14	chr5:93974600-93993400	Strong transcription	Hela-S3	cervix
15	chr5:93975600-93995200	Weak transcription	Esophagus	oesophagus
16	chr5:93975600-93995200	Weak transcription	Fetal Stomach	stomach
17	chr5:93975600-94012000	Weak transcription	Aorta	Aorta
18	chr5:93975800-93993400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr5:93975800-93994000	Weak transcription	Small Intestine	intestine
20	chr5:93976800-94025000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr5:93977000-93993600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr5:93977400-93993600	Weak transcription	K562	blood
23	chr5:93977800-93995400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:93978000-93995000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:93981000-94012000	Weak transcription	Left Ventricle	heart
26	chr5:93982600-93995400	Weak transcription	Pancreas	Pancrea
27	chr5:93985600-93993200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr5:93987600-93995400	Strong transcription	Fetal Thymus	thymus
29	chr5:93988400-93996200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:93988600-93997800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:93988800-93995800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:93989000-93995600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:93989800-93994200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:93989800-93995200	Weak transcription	Fetal Intestine Small	intestine
35	chr5:93990200-93994400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:93990200-93995800	ZNF genes & repeats	A549	lung
37	chr5:93990400-93994600	ZNF genes & repeats	Dnd41	blood
38	chr5:93990600-93995600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
39	chr5:93990600-93995800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
40	chr5:93990600-93996200	ZNF genes & repeats	Primary B cells from cord blood	blood
41	chr5:93990600-94008200	Weak transcription	Colon Smooth Muscle	Colon
42	chr5:93990800-93994600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr5:93990800-93994800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
44	chr5:93991200-93993200	Weak transcription	Brain Hippocampus Middle	brain
45	chr5:93991200-93993200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr5:93991200-93993400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:93991200-93993600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr5:93991200-93993600	Weak transcription	Adipose Nuclei	Adipose
49	chr5:93991200-93993600	Weak transcription	Osteobl	bone
50	chr5:93991200-93995400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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