Variant report

Variant	rs10078049
Chromosome Location	chr5:94039106-94039107
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:49)

rs_ID	r²[population]
rs10035632	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10037228	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10041262	0.87[ASN][1000 genomes]
rs10041551	0.90[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041843	0.87[ASN][1000 genomes]
rs10044797	0.89[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10051931	0.85[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053484	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10056685	0.81[CEU][hapmap]
rs10058130	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10058618	0.89[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061737	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062248	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070258	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs10076188	0.90[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10076461	0.87[ASN][1000 genomes]
rs10078304	0.85[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10476612	0.80[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10476613	0.89[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10476615	0.90[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11949227	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11955373	0.85[CEU][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960129	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12516225	0.80[EUR][1000 genomes]
rs12517866	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12518034	0.80[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12522312	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13169956	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13353994	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13354061	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13358642	0.94[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13361811	0.85[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13362556	0.89[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28645132	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28787271	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs306573	0.90[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs306575	0.90[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869218	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55974730	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6862592	0.87[ASN][1000 genomes]
rs6873364	1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6879307	0.80[EUR][1000 genomes]
rs755898	0.85[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7705424	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs7725095	0.84[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725698	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7731360	0.89[EUR][1000 genomes]
rs7737779	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9314118	0.81[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10078049	ANKRD32	cis	multi-tissue	Pritchard
rs10078049	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL
rs10078049	MCTP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 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	chr5:93995600-94050400	Weak transcription	Esophagus	oesophagus
5	chr5:93996600-94048400	Weak transcription	Lung	lung
6	chr5:94012600-94048400	Weak transcription	Aorta	Aorta
7	chr5:94012600-94048400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:94012600-94049000	Weak transcription	Left Ventricle	heart
9	chr5:94012600-94051000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:94012600-94053600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:94020200-94048400	Weak transcription	Psoas Muscle	Psoas
12	chr5:94020800-94050000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:94023200-94045600	Weak transcription	Primary B cells from cord blood	blood
14	chr5:94023200-94046400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:94023200-94049800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:94023200-94050400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr5:94023200-94051000	Weak transcription	Thymus	Thymus
18	chr5:94023400-94044200	Weak transcription	Primary T cells from cord blood	blood
19	chr5:94023400-94045000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr5:94023400-94050400	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:94023400-94051800	Weak transcription	Fetal Intestine Small	intestine
22	chr5:94024600-94046600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr5:94024600-94051800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr5:94025800-94046200	Weak transcription	Adipose Nuclei	Adipose
25	chr5:94025800-94050800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:94025800-94050800	Weak transcription	K562	blood
27	chr5:94025800-94051400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:94026400-94051600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr5:94028000-94043000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:94028000-94050600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:94028000-94051600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:94028800-94040200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr5:94029000-94051400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:94029200-94045800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:94029200-94049000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:94029200-94050400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr5:94029200-94051800	Weak transcription	Brain Germinal Matrix	brain
38	chr5:94029200-94052400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:94029400-94040400	Weak transcription	A549	lung
40	chr5:94029400-94048800	Weak transcription	HMEC	breast
41	chr5:94029400-94051200	Weak transcription	Fetal Brain Male	brain
42	chr5:94029400-94051400	Weak transcription	Fetal Heart	heart
43	chr5:94029800-94040800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr5:94029800-94050000	Weak transcription	Osteobl	bone
45	chr5:94030200-94051400	Weak transcription	HSMM	muscle
46	chr5:94031000-94045600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr5:94031000-94047400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:94031000-94050000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:94031000-94050000	Weak transcription	Liver	Liver
50	chr5:94031000-94051200	Weak transcription	Duodenum Mucosa	Duodenum

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