Variant report

Variant	rs816142
Chromosome Location	chr13:96638636-96638637
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96632367..96634292-chr13:96635472..96638810,3	K562	blood:
2	chr13:96632367..96634450-chr13:96637310..96639783,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10508027	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs11616953	0.80[EUR][1000 genomes]
rs11618108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs11619636	0.90[ASN][1000 genomes]
rs12428062	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs12430152	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs1330556	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1330557	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs16951448	0.90[ASN][1000 genomes]
rs1788062	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1854758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2170813	1.00[CEU][hapmap]
rs3099362	0.92[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.81[ASN][1000 genomes]
rs3099363	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3101570	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs4254181	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4347496	0.81[AFR][1000 genomes]
rs4383020	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs4409947	0.85[JPT][hapmap]
rs4526890	0.81[ASN][1000 genomes]
rs4547219	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs475882	0.88[CEU][hapmap]
rs476954	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4773932	0.90[ASN][1000 genomes]
rs495214	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs526702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs531549	0.90[ASN][1000 genomes]
rs534010	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs534429	1.00[CEU][hapmap]
rs537463	0.90[ASN][1000 genomes]
rs540213	1.00[CEU][hapmap]
rs56077337	0.90[ASN][1000 genomes]
rs565297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs565851	1.00[CEU][hapmap]
rs565898	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs645595	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs651812	0.86[ASN][1000 genomes]
rs661544	0.90[ASN][1000 genomes]
rs662884	1.00[CEU][hapmap];0.90[ASN][1000 genomes]
rs674565	1.00[CEU][hapmap]
rs675144	1.00[CEU][hapmap]
rs72636541	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72636556	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72636562	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72636570	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7323408	0.86[JPT][hapmap]
rs7331211	0.86[JPT][hapmap]
rs7331549	0.86[JPT][hapmap]
rs7332078	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7334320	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7335209	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7339059	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7999737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8000018	0.81[ASN][1000 genomes]
rs9516621	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9516625	0.88[CEU][hapmap]
rs9525077	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9525079	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9584324	0.86[JPT][hapmap]
rs9590344	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832691	chr13:96478098-96659823	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1051574	chr13:96550653-96779248	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1040320	chr13:96573646-96790859	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv869471	chr13:96622327-97223956	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs816142	UGGT2	cis	cerebellum	SCAN
rs816142	DZIP1	cis	parietal	SCAN
rs816142	DZIP1	cis	Artery Tibial	GTEx
rs816142	UGCGL2	cis	multi-tissue	Pritchard

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96612200-96655000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr13:96612200-96668600	Weak transcription	Pancreas	Pancrea
3	chr13:96613200-96694200	Weak transcription	A549	lung
4	chr13:96613400-96641600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr13:96613400-96643000	Weak transcription	Right Ventricle	heart
6	chr13:96613600-96650000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr13:96613600-96663600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr13:96614000-96652400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr13:96616200-96668600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr13:96616800-96668400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr13:96617000-96649000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr13:96617000-96663200	Weak transcription	NHDF-Ad	bronchial
13	chr13:96618800-96654200	Weak transcription	Fetal Lung	lung
14	chr13:96621600-96668600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr13:96622000-96668600	Weak transcription	Aorta	Aorta
16	chr13:96622200-96660400	Weak transcription	Ovary	ovary
17	chr13:96622200-96668600	Weak transcription	Fetal Kidney	kidney
18	chr13:96622200-96671400	Weak transcription	Hela-S3	cervix
19	chr13:96622200-96677200	Weak transcription	NH-A	brain
20	chr13:96622400-96668200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr13:96622800-96647800	Weak transcription	HSMM	muscle
22	chr13:96623600-96668200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr13:96627000-96643400	Weak transcription	HepG2	liver
24	chr13:96628600-96639800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr13:96630200-96660400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr13:96630400-96639400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr13:96632400-96657600	Weak transcription	GM12878-XiMat	blood
28	chr13:96632800-96657800	Weak transcription	Fetal Muscle Leg	muscle
29	chr13:96634000-96639400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr13:96634800-96644600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr13:96634800-96668200	Weak transcription	Fetal Stomach	stomach
32	chr13:96635000-96640000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr13:96635200-96641000	Weak transcription	Brain Hippocampus Middle	brain
34	chr13:96635200-96643200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:96635600-96657400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr13:96635600-96657600	Weak transcription	Left Ventricle	heart
37	chr13:96635600-96659200	Weak transcription	Adipose Nuclei	Adipose
38	chr13:96635800-96655200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr13:96636000-96650400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr13:96636400-96659000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr13:96638200-96647600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr13:96638400-96647800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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