Variant report

Variant	rs2112449
Chromosome Location	chr5:94019780-94019781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10037940	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10039102	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10039797	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10052066	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10062402	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10072894	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10074178	0.81[AMR][1000 genomes]
rs10078522	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1031389	0.93[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs10476614	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1124667	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11948061	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12189060	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1451734	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1549179	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2112448	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2112450	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2636	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2638	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs306574	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs306578	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs306580	0.89[GIH][hapmap]
rs395097	0.94[JPT][hapmap]
rs421521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs432449	0.83[GIH][hapmap]
rs6556849	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs747880	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs755899	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs755901	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7709494	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]
rs7735924	0.82[CEU][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][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	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
6	nsv964782	chr5:94019632-94020856	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2112449	MCTP1	cis	Temporal Cortex	GTEx
rs2112449	MCTP1	cis	uninvolved skin	skin_eQTL
rs2112449	MCTP1	cis	lesional skin	skin_eQTL
rs2112449	ANKRD32	cis	parietal	SCAN
rs2112449	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs2112449	C5orf36	cis	cerebellum	SCAN
rs2112449	MCTP1	cis	normal skin	skin_eQTL
rs2112449	MCTP1	cis	lymphoblastoid	seeQTL
rs2112449	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL
rs2112449	MCTP1	cis	Cerebellum	GTEx

Chromatin state (count:104 , 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	chr5:93976800-94025000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:93991200-94049000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr5:93994200-94030800	Weak transcription	Right Ventricle	heart
5	chr5:93994200-94047200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:93994400-94022600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr5:93994400-94025400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:93994400-94027600	Weak transcription	Liver	Liver
9	chr5:93994400-94027600	Weak transcription	NHDF-Ad	bronchial
10	chr5:93994400-94029000	Weak transcription	Brain Hippocampus Middle	brain
11	chr5:93994400-94048800	Weak transcription	Small Intestine	intestine
12	chr5:93994600-94026600	Weak transcription	Fetal Kidney	kidney
13	chr5:93994600-94029200	Weak transcription	Brain Anterior Caudate	brain
14	chr5:93994600-94032200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr5:93995400-94024800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr5:93995600-94024400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:93995600-94033000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr5:93995600-94050400	Weak transcription	Esophagus	oesophagus
19	chr5:93996000-94024000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr5:93996000-94027600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:93996000-94036000	Weak transcription	GM12878-XiMat	blood
22	chr5:93996200-94026600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:93996200-94029800	Weak transcription	Ovary	ovary
24	chr5:93996600-94023000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:93996600-94027800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:93996600-94048400	Weak transcription	Lung	lung
27	chr5:93996800-94036200	Weak transcription	Gastric	stomach
28	chr5:93997000-94033800	Weak transcription	Placenta	Placenta
29	chr5:94001000-94030000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr5:94001200-94022400	Weak transcription	Fetal Stomach	stomach
31	chr5:94001200-94023000	Weak transcription	Adipose Nuclei	Adipose
32	chr5:94001600-94024200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:94001800-94022400	Weak transcription	Thymus	Thymus
34	chr5:94001800-94027600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:94002000-94022200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr5:94003800-94023000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:94004000-94022600	Weak transcription	Fetal Intestine Large	intestine
38	chr5:94004600-94022400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr5:94007200-94025800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr5:94008600-94038600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr5:94008800-94027600	Weak transcription	Osteobl	bone
42	chr5:94009000-94024200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr5:94009600-94022600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr5:94010600-94027800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:94010800-94022200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr5:94010800-94022400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:94010800-94022400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr5:94010800-94024200	Strong transcription	Hela-S3	cervix
49	chr5:94010800-94024400	Weak transcription	Fetal Brain Male	brain
50	chr5:94010800-94024800	Weak transcription	HMEC	breast

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