Variant report

Variant	rs306572
Chromosome Location	chr5:94032122-94032123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17084010	0.94[CEU][hapmap];0.90[TSI][hapmap]
rs2973154	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs430555	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62365699	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72773602	0.91[EUR][1000 genomes]
rs7707464	0.82[CHB][hapmap];1.00[CHD][hapmap];0.96[MKK][hapmap]
rs845725	1.00[CHB][hapmap];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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs306572	MCTP1	cis	multi-tissue	Pritchard
rs306572	MCTP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93991200-94049000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:93994200-94047200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr5:93994400-94048800	Weak transcription	Small Intestine	intestine
4	chr5:93994600-94032200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr5:93995600-94033000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr5:93995600-94050400	Weak transcription	Esophagus	oesophagus
7	chr5:93996000-94036000	Weak transcription	GM12878-XiMat	blood
8	chr5:93996600-94048400	Weak transcription	Lung	lung
9	chr5:93996800-94036200	Weak transcription	Gastric	stomach
10	chr5:93997000-94033800	Weak transcription	Placenta	Placenta
11	chr5:94008600-94038600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:94012600-94034000	Weak transcription	Pancreas	Pancrea
13	chr5:94012600-94035000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:94012600-94048400	Weak transcription	Aorta	Aorta
15	chr5:94012600-94048400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr5:94012600-94049000	Weak transcription	Left Ventricle	heart
17	chr5:94012600-94051000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr5:94012600-94053600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr5:94013000-94032400	Weak transcription	HepG2	liver
20	chr5:94020200-94048400	Weak transcription	Psoas Muscle	Psoas
21	chr5:94020800-94050000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:94022800-94032400	Strong transcription	Dnd41	blood
23	chr5:94023200-94045600	Weak transcription	Primary B cells from cord blood	blood
24	chr5:94023200-94046400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:94023200-94049800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr5:94023200-94050400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr5:94023200-94051000	Weak transcription	Thymus	Thymus
28	chr5:94023400-94032600	Weak transcription	Fetal Intestine Large	intestine
29	chr5:94023400-94035600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:94023400-94044200	Weak transcription	Primary T cells from cord blood	blood
31	chr5:94023400-94045000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr5:94023400-94050400	Weak transcription	Fetal Muscle Leg	muscle
33	chr5:94023400-94051800	Weak transcription	Fetal Intestine Small	intestine
34	chr5:94024600-94046600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr5:94024600-94051800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr5:94025800-94036200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr5:94025800-94037800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:94025800-94046200	Weak transcription	Adipose Nuclei	Adipose
39	chr5:94025800-94050800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:94025800-94050800	Weak transcription	K562	blood
41	chr5:94025800-94051400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr5:94026000-94038400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr5:94026400-94051600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr5:94027000-94034000	Weak transcription	Fetal Kidney	kidney
45	chr5:94028000-94032600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:94028000-94038600	Weak transcription	Fetal Lung	lung
47	chr5:94028000-94043000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr5:94028000-94050600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:94028000-94051600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:94028200-94037200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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