Variant report

Variant	rs7178988
Chromosome Location	chr15:34482862-34482863
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10775222	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs10851950	0.81[ASN][1000 genomes]
rs10851952	0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs10851955	0.91[ASN][1000 genomes]
rs11073010	0.91[ASN][1000 genomes]
rs11073014	0.91[ASN][1000 genomes]
rs11073019	0.88[ASN][1000 genomes]
rs11635964	0.88[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs11636442	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs11852537	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11854686	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11857205	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11857684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11858408	0.88[ASN][1000 genomes]
rs12437551	0.80[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs12441003	0.92[ASN][1000 genomes]
rs12442758	0.89[ASN][1000 genomes]
rs12591181	0.90[JPT][hapmap]
rs12592460	0.83[ASN][1000 genomes]
rs12594077	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs12917397	0.94[ASN][1000 genomes]
rs16958829	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs16958835	0.89[YRI][hapmap]
rs16958836	0.90[YRI][hapmap]
rs16958848	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1836978	0.82[ASN][1000 genomes]
rs1978810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2339368	0.83[ASN][1000 genomes]
rs28375867	0.85[ASN][1000 genomes]
rs28418847	0.85[ASN][1000 genomes]
rs28538047	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28652966	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28813796	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34187931	0.85[ASN][1000 genomes]
rs4381574	0.88[ASN][1000 genomes]
rs4780226	0.81[ASN][1000 genomes]
rs4780227	0.90[ASN][1000 genomes]
rs4780229	0.89[ASN][1000 genomes]
rs56731918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57502425	0.81[ASN][1000 genomes]
rs57530092	0.85[ASN][1000 genomes]
rs57834992	0.85[ASN][1000 genomes]
rs58875083	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59635553	0.85[ASN][1000 genomes]
rs60749797	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60905714	0.85[ASN][1000 genomes]
rs6495580	0.85[ASN][1000 genomes]
rs7172633	0.85[ASN][1000 genomes]
rs7173244	0.84[ASN][1000 genomes]
rs7173618	0.85[ASN][1000 genomes]
rs7174442	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.85[ASN][1000 genomes]
rs7174586	0.84[ASN][1000 genomes]
rs7175168	0.83[ASN][1000 genomes]
rs7178002	0.93[YRI][hapmap];0.85[ASN][1000 genomes]
rs7178203	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.85[ASN][1000 genomes]
rs7180024	0.85[ASN][1000 genomes]
rs7180920	0.83[ASN][1000 genomes]
rs7181687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73376164	0.80[ASN][1000 genomes]
rs73378128	0.85[ASN][1000 genomes]
rs73378138	0.85[ASN][1000 genomes]
rs73378141	0.84[ASN][1000 genomes]
rs73380107	0.82[ASN][1000 genomes]
rs73380126	0.85[ASN][1000 genomes]
rs73380135	0.85[ASN][1000 genomes]
rs73380141	0.85[ASN][1000 genomes]
rs73380157	0.85[ASN][1000 genomes]
rs7497840	0.83[ASN][1000 genomes]
rs7497951	0.84[ASN][1000 genomes]
rs8025406	0.93[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs8025730	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.82[ASN][1000 genomes]
rs8026939	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8027499	0.81[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs8027830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028932	0.85[ASN][1000 genomes]
rs8028950	0.85[ASN][1000 genomes]
rs8031102	0.82[ASN][1000 genomes]
rs8034315	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8035493	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs8036468	0.86[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs8040732	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs8043216	0.87[CHB][hapmap];0.83[JPT][hapmap];0.96[ASN][1000 genomes]
rs9920654	0.81[ASN][1000 genomes]
rs9944206	0.85[ASN][1000 genomes]
rs9972505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035579	chr15:34363159-34501115	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats 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	15 gene(s)	inside rSNPs	diseases
2	esv3507159	chr15:34456709-34485891	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
3	esv3507160	chr15:34456709-34485891	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7178988	C15orf29	cis	normal skin	skin_eQTL
rs7178988	NOP10	cis	Thyroid	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34454200-34497800	Weak transcription	Osteobl	bone
2	chr15:34454600-34501200	Weak transcription	Colonic Mucosa	Colon
3	chr15:34454800-34501000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr15:34464600-34500400	Weak transcription	Hela-S3	cervix
5	chr15:34466400-34500400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:34467000-34500800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr15:34467200-34491400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:34467200-34500200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:34467400-34486200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:34468000-34496400	Weak transcription	Fetal Lung	lung
11	chr15:34468000-34497800	Weak transcription	NHEK	skin
12	chr15:34468200-34485800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr15:34468200-34498000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr15:34471000-34501000	Weak transcription	Aorta	Aorta
15	chr15:34471600-34500400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr15:34473400-34500400	Weak transcription	HSMMtube	muscle
17	chr15:34475000-34500400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:34475400-34483200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr15:34475400-34491600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:34475600-34491800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:34475600-34493600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr15:34475600-34495600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:34475600-34499800	Weak transcription	Ovary	ovary
24	chr15:34475600-34500000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr15:34475600-34500400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:34475600-34500400	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:34475600-34500400	Weak transcription	HUVEC	blood vessel
28	chr15:34476000-34491600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr15:34476000-34491800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:34476200-34499600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr15:34476200-34500000	Weak transcription	Fetal Brain Female	brain
32	chr15:34476400-34500800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:34476800-34499800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr15:34477000-34499800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr15:34477200-34500000	Weak transcription	Liver	Liver
36	chr15:34477600-34501000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:34477600-34501200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr15:34478000-34491200	Weak transcription	Fetal Muscle Leg	muscle
39	chr15:34478000-34500200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:34478200-34492000	Weak transcription	Primary B cells from cord blood	blood
41	chr15:34478400-34489000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:34478600-34491800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr15:34478600-34496400	Weak transcription	HSMM	muscle
44	chr15:34478800-34491600	Weak transcription	Primary T cells from cord blood	blood
45	chr15:34478800-34500000	Weak transcription	Fetal Intestine Large	intestine
46	chr15:34478800-34500400	Weak transcription	Thymus	Thymus
47	chr15:34478800-34500800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr15:34479000-34488400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr15:34479000-34498200	Weak transcription	NH-A	brain
50	chr15:34479200-34500000	Weak transcription	Esophagus	oesophagus

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