Variant report

Variant	rs10039102
Chromosome Location	chr5:94032995-94032996
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10037940	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10039797	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10052066	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10062402	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10072894	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10078522	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10476614	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1124667	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11948061	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12189060	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1451734	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1549179	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2112448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2112449	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2112450	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2636	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs306574	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs306578	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs421521	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6556849	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs747880	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs755899	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs755901	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7709494	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7735924	0.86[AMR][1000 genomes];0.90[EUR][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
rs10039102	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs10039102	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 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	chr5:93995600-94033000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr5:93995600-94050400	Weak transcription	Esophagus	oesophagus
6	chr5:93996000-94036000	Weak transcription	GM12878-XiMat	blood
7	chr5:93996600-94048400	Weak transcription	Lung	lung
8	chr5:93996800-94036200	Weak transcription	Gastric	stomach
9	chr5:93997000-94033800	Weak transcription	Placenta	Placenta
10	chr5:94008600-94038600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:94012600-94034000	Weak transcription	Pancreas	Pancrea
12	chr5:94012600-94035000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:94012600-94048400	Weak transcription	Aorta	Aorta
14	chr5:94012600-94048400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:94012600-94049000	Weak transcription	Left Ventricle	heart
16	chr5:94012600-94051000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr5:94012600-94053600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:94020200-94048400	Weak transcription	Psoas Muscle	Psoas
19	chr5:94020800-94050000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:94023200-94045600	Weak transcription	Primary B cells from cord blood	blood
21	chr5:94023200-94046400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:94023200-94049800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:94023200-94050400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:94023200-94051000	Weak transcription	Thymus	Thymus
25	chr5:94023400-94035600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:94023400-94044200	Weak transcription	Primary T cells from cord blood	blood
27	chr5:94023400-94045000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr5:94023400-94050400	Weak transcription	Fetal Muscle Leg	muscle
29	chr5:94023400-94051800	Weak transcription	Fetal Intestine Small	intestine
30	chr5:94024600-94046600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:94024600-94051800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:94025800-94036200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr5:94025800-94037800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr5:94025800-94046200	Weak transcription	Adipose Nuclei	Adipose
35	chr5:94025800-94050800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr5:94025800-94050800	Weak transcription	K562	blood
37	chr5:94025800-94051400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr5:94026000-94038400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr5:94026400-94051600	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:94027000-94034000	Weak transcription	Fetal Kidney	kidney
41	chr5:94028000-94038600	Weak transcription	Fetal Lung	lung
42	chr5:94028000-94043000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:94028000-94050600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:94028000-94051600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:94028200-94037200	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr5:94028800-94040200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr5:94029000-94033200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr5:94029000-94051400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr5:94029200-94045800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr5:94029200-94049000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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