Variant report

Variant	rs7709494
Chromosome Location	chr5:94006023-94006024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10037940	0.96[CEU][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.86[TSI][hapmap];0.96[EUR][1000 genomes]
rs10039102	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10039797	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10052066	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062402	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10072894	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10074178	0.82[AMR][1000 genomes]
rs10078522	1.00[CEU][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1031389	0.93[CEU][hapmap];0.82[AMR][1000 genomes]
rs10476614	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1124667	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948061	0.85[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189060	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1451734	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1549179	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112448	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2112449	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2112450	0.82[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636	0.82[CEU][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs2638	0.81[CEU][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs306574	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs306578	0.88[EUR][1000 genomes]
rs395097	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs421521	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6556849	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs747880	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs755899	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs755901	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7735924	0.82[CEU][hapmap];0.87[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7709494	MCTP1	cis	normal skin	skin_eQTL
rs7709494	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL
rs7709494	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs7709494	MCTP1	cis	Temporal Cortex	GTEx
rs7709494	MCTP1	cis	Cerebellum	GTEx
rs7709494	MCTP1	cis	uninvolved skin	skin_eQTL
rs7709494	MCTP1	cis	lesional skin	skin_eQTL

Chromatin state (count:101 , 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	chr5:93969400-94008400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr5:93975600-94012000	Weak transcription	Aorta	Aorta
4	chr5:93976800-94025000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:93981000-94012000	Weak transcription	Left Ventricle	heart
6	chr5:93990600-94008200	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:93991200-94049000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:93994200-94010200	Weak transcription	NHEK	skin
9	chr5:93994200-94012000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:93994200-94030800	Weak transcription	Right Ventricle	heart
11	chr5:93994200-94047200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:93994400-94006200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:93994400-94012000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr5:93994400-94022600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:93994400-94025400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr5:93994400-94027600	Weak transcription	Liver	Liver
17	chr5:93994400-94027600	Weak transcription	NHDF-Ad	bronchial
18	chr5:93994400-94029000	Weak transcription	Brain Hippocampus Middle	brain
19	chr5:93994400-94048800	Weak transcription	Small Intestine	intestine
20	chr5:93994600-94007400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:93994600-94026600	Weak transcription	Fetal Kidney	kidney
22	chr5:93994600-94029200	Weak transcription	Brain Anterior Caudate	brain
23	chr5:93994600-94032200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr5:93995400-94012000	Weak transcription	HepG2	liver
25	chr5:93995400-94024800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr5:93995600-94009600	Weak transcription	Fetal Brain Female	brain
27	chr5:93995600-94024400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:93995600-94033000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:93995600-94050400	Weak transcription	Esophagus	oesophagus
30	chr5:93995800-94010600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:93995800-94012000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr5:93995800-94012000	Weak transcription	HSMM	muscle
33	chr5:93996000-94024000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr5:93996000-94027600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:93996000-94036000	Weak transcription	GM12878-XiMat	blood
36	chr5:93996200-94007400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:93996200-94026600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:93996200-94029800	Weak transcription	Ovary	ovary
39	chr5:93996400-94008000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr5:93996400-94012000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr5:93996600-94012000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr5:93996600-94019200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:93996600-94023000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:93996600-94027800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr5:93996600-94048400	Weak transcription	Lung	lung
46	chr5:93996800-94013800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:93996800-94036200	Weak transcription	Gastric	stomach
48	chr5:93997000-94008000	Strong transcription	Hela-S3	cervix
49	chr5:93997000-94012000	Weak transcription	Spleen	Spleen
50	chr5:93997000-94033800	Weak transcription	Placenta	Placenta

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