Variant report

Variant	rs533143
Chromosome Location	chr15:44188854-44188855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44185248..44189822-chr15:44193811..44195914,4	K562	blood:
2	chr15:44188604..44190452-chr15:44190792..44193773,2	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10163054	0.95[CHB][hapmap];0.92[CHD][hapmap]
rs10438303	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs1053492	1.00[CEU][hapmap]
rs11070408	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap]
rs11070410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[TSI][hapmap]
rs11638972	1.00[CEU][hapmap]
rs11852767	0.90[ASN][1000 genomes]
rs11856495	0.83[ASN][1000 genomes]
rs11856795	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[ASN][1000 genomes]
rs12440573	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs12441127	1.00[CHB][hapmap]
rs12441861	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs12441984	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs12702	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs16950562	1.00[CHB][hapmap]
rs16965120	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs16977724	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs16977798	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1965795	0.85[ASN][1000 genomes]
rs2277531	1.00[CHB][hapmap]
rs2412823	0.82[CEU][hapmap]
rs2467402	0.95[CHB][hapmap];0.94[CHD][hapmap]
rs2788	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs28413704	0.85[ASN][1000 genomes]
rs28437196	0.84[ASN][1000 genomes]
rs28476182	0.84[ASN][1000 genomes]
rs28509275	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs28513374	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs28519630	0.85[ASN][1000 genomes]
rs28524541	0.84[ASN][1000 genomes]
rs28531819	0.84[ASN][1000 genomes]
rs28564774	0.84[ASN][1000 genomes]
rs28590651	0.81[ASN][1000 genomes]
rs28636829	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs28679673	0.84[ASN][1000 genomes]
rs28684672	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs28687459	0.84[ASN][1000 genomes]
rs28696802	0.84[ASN][1000 genomes]
rs28707214	0.84[ASN][1000 genomes]
rs28780699	0.84[ASN][1000 genomes]
rs28823973	0.90[ASN][1000 genomes]
rs28858500	0.88[ASN][1000 genomes]
rs28866846	0.86[ASN][1000 genomes]
rs2927085	0.86[CEU][hapmap]
rs2955969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3087657	1.00[CEU][hapmap];0.80[TSI][hapmap]
rs3736180	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs3742982	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3759790	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs3759791	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap]
rs3816792	0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[ASN][1000 genomes]
rs3825783	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs3862142	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs4997480	1.00[CHB][hapmap]
rs524908	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56909447	0.84[ASN][1000 genomes]
rs575082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs61390361	0.86[ASN][1000 genomes]
rs663214	1.00[CEU][hapmap]
rs667476	0.91[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68079546	0.84[ASN][1000 genomes]
rs686666	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs688009	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs693919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs694461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs7169322	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs7169988	0.90[CHB][hapmap]
rs7171750	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7174208	1.00[CHB][hapmap]
rs7175032	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs7175129	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7179388	0.84[ASN][1000 genomes]
rs7183809	0.84[ASN][1000 genomes]
rs8023458	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs8023508	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs8032649	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs8040839	0.83[ASN][1000 genomes]
rs9944216	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[ASN][1000 genomes]
rs9989313	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][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	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
5	nsv1050263	chr15:44093927-44204047	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a
6	nsv1044435	chr15:44176103-44507403	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs533143	ZSCAN29	cis	Thyroid	GTEx
rs533143	TGM5	cis	lymphoblastoid	seeQTL
rs533143	ZNF690	cis	multi-tissue	Pritchard
rs533143	WDR76	cis	parietal	SCAN
rs533143	STRC	cis	multi-tissue	Pritchard
rs533143	ADAL	cis	parietal	SCAN
rs533143	AC011330.5	cis	Thyroid	GTEx
rs533143	DUOX2	cis	parietal	SCAN
rs533143	CKMT1A	cis	Esophagus Mucosa	GTEx
rs533143	STRCP1	cis	Whole Blood	GTEx
rs533143	SERF2	cis	lymphoblastoid	seeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44156800-44206400	Weak transcription	Fetal Brain Male	brain
2	chr15:44166800-44193800	Weak transcription	Spleen	Spleen
3	chr15:44166800-44196200	Weak transcription	Osteobl	bone
4	chr15:44173600-44208000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:44173800-44190000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:44173800-44193600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:44173800-44211600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:44174200-44194200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr15:44174200-44195800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr15:44174200-44195800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:44174200-44211600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr15:44176600-44192000	Weak transcription	Hela-S3	cervix
13	chr15:44176800-44193600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:44177200-44192000	Weak transcription	A549	lung
15	chr15:44177200-44192800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:44178200-44197800	Weak transcription	NHLF	lung
17	chr15:44178400-44189400	Enhancers	Fetal Heart	heart
18	chr15:44179000-44192000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:44179400-44193600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:44180000-44195800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:44180800-44192400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr15:44183200-44193000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:44183400-44191800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:44183400-44197800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:44184000-44194200	Weak transcription	HUVEC	blood vessel
26	chr15:44184400-44190400	Weak transcription	Brain Germinal Matrix	brain
27	chr15:44184800-44190800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:44186200-44193200	Weak transcription	HMEC	breast
29	chr15:44186200-44197800	Weak transcription	NHEK	skin
30	chr15:44186400-44190600	Weak transcription	Ovary	ovary
31	chr15:44186400-44191000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr15:44186600-44192000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:44186800-44189000	Weak transcription	HSMM	muscle
34	chr15:44186800-44190600	Weak transcription	Fetal Stomach	stomach
35	chr15:44187000-44190600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:44187000-44190800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:44187000-44203600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr15:44187200-44191200	Weak transcription	Right Ventricle	heart
39	chr15:44187400-44190000	Enhancers	Brain Substantia Nigra	brain
40	chr15:44187600-44189000	Enhancers	Brain Angular Gyrus	brain
41	chr15:44187600-44196000	Weak transcription	Fetal Muscle Leg	muscle
42	chr15:44187800-44189200	Strong transcription	NH-A	brain
43	chr15:44187800-44195800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:44188000-44191800	Weak transcription	Left Ventricle	heart
45	chr15:44188000-44192600	Weak transcription	HSMMtube	muscle
46	chr15:44188200-44189000	Weak transcription	Brain Anterior Caudate	brain
47	chr15:44188200-44189400	Enhancers	Brain Cingulate Gyrus	brain
48	chr15:44188200-44190000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:44188200-44191200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr15:44188400-44189000	Strong transcription	Fetal Brain Female	brain

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