Variant report

Variant	rs55974730
Chromosome Location	chr5:94008858-94008859
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10035632	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10037228	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10041262	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10041551	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10041843	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10044797	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10051931	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10053484	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10056685	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10058130	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10058618	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10061737	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10062248	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10070258	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10076188	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10076461	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10078049	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10078304	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10476612	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10476613	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10476615	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11949227	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11955373	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11960129	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12516225	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12517866	0.83[EUR][1000 genomes]
rs12518034	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12522312	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13169956	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13353994	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13354061	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13358642	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13361811	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13362556	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28645132	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28787271	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs306573	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs306575	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4869218	0.90[EUR][1000 genomes]
rs6862592	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6873364	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6879307	0.89[EUR][1000 genomes]
rs755898	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7705424	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7725095	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7725698	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7731360	0.82[EUR][1000 genomes]
rs7737779	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv882387	chr5:94001476-94071404	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs55974730	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs55974730	ANKRD32	cis	multi-tissue	Pritchard
rs55974730	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93955800-94027600	Weak transcription	NH-A	brain
2	chr5:93975600-94012000	Weak transcription	Aorta	Aorta
3	chr5:93976800-94025000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr5:93981000-94012000	Weak transcription	Left Ventricle	heart
5	chr5:93991200-94049000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:93994200-94010200	Weak transcription	NHEK	skin
7	chr5:93994200-94012000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:93994200-94030800	Weak transcription	Right Ventricle	heart
9	chr5:93994200-94047200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr5:93994400-94012000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:93994400-94022600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr5:93994400-94025400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr5:93994400-94027600	Weak transcription	Liver	Liver
14	chr5:93994400-94027600	Weak transcription	NHDF-Ad	bronchial
15	chr5:93994400-94029000	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:93994400-94048800	Weak transcription	Small Intestine	intestine
17	chr5:93994600-94026600	Weak transcription	Fetal Kidney	kidney
18	chr5:93994600-94029200	Weak transcription	Brain Anterior Caudate	brain
19	chr5:93994600-94032200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr5:93995400-94012000	Weak transcription	HepG2	liver
21	chr5:93995400-94024800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr5:93995600-94009600	Weak transcription	Fetal Brain Female	brain
23	chr5:93995600-94024400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:93995600-94033000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr5:93995600-94050400	Weak transcription	Esophagus	oesophagus
26	chr5:93995800-94010600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr5:93995800-94012000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr5:93995800-94012000	Weak transcription	HSMM	muscle
29	chr5:93996000-94024000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr5:93996000-94027600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:93996000-94036000	Weak transcription	GM12878-XiMat	blood
32	chr5:93996200-94026600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr5:93996200-94029800	Weak transcription	Ovary	ovary
34	chr5:93996400-94012000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:93996600-94012000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr5:93996600-94019200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:93996600-94023000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:93996600-94027800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr5:93996600-94048400	Weak transcription	Lung	lung
40	chr5:93996800-94013800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:93996800-94036200	Weak transcription	Gastric	stomach
42	chr5:93997000-94012000	Weak transcription	Spleen	Spleen
43	chr5:93997000-94033800	Weak transcription	Placenta	Placenta
44	chr5:93997400-94012000	Weak transcription	Pancreas	Pancrea
45	chr5:93997600-94010400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr5:94001000-94030000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr5:94001200-94010400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr5:94001200-94012000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr5:94001200-94012000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr5:94001200-94012000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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