Variant report

Variant	rs816139
Chromosome Location	chr13:96622673-96622674
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1807900	0.84[EUR][1000 genomes]
rs1980942	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1996054	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2389530	0.80[TSI][hapmap]
rs2389531	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2774113	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3099358	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs3099359	0.82[ASW][hapmap];0.85[YRI][hapmap]
rs3099360	1.00[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs34482628	0.81[EUR][1000 genomes]
rs472788	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs473930	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4773927	0.91[ASW][hapmap]
rs4773930	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs493109	0.87[CEU][hapmap];0.95[CHB][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs506474	0.89[EUR][1000 genomes]
rs509572	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs517173	0.88[EUR][1000 genomes]
rs521235	0.88[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs527680	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs529306	0.83[CEU][hapmap];0.91[CHB][hapmap];0.89[EUR][1000 genomes]
rs531090	0.89[EUR][1000 genomes]
rs532399	0.89[EUR][1000 genomes]
rs536606	0.89[EUR][1000 genomes]
rs537571	0.82[EUR][1000 genomes]
rs539604	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs541811	0.91[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs544080	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs551457	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs552598	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs561996	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs566894	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576184	0.82[ASW][hapmap];0.85[YRI][hapmap]
rs590758	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs592205	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs595696	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs6492826	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7333045	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7992824	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7994626	0.85[YRI][hapmap]
rs7998903	0.85[YRI][hapmap]
rs816143	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9516620	0.85[YRI][hapmap]
rs9516626	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9516629	0.84[EUR][1000 genomes]
rs9525081	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9525085	0.91[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9525086	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9525091	0.83[EUR][1000 genomes]
rs9525093	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9525095	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs9525098	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9561979	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9742440	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv900935	chr13:96497070-96631221	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs816139	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL
rs816139	DNAJC3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96577000-96623200	Weak transcription	NHLF	lung
2	chr13:96599000-96623600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr13:96609400-96623600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr13:96609800-96636200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr13:96612200-96622800	Weak transcription	Spleen	Spleen
6	chr13:96612200-96623600	Weak transcription	Placenta	Placenta
7	chr13:96612200-96655000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr13:96612200-96668600	Weak transcription	Pancreas	Pancrea
9	chr13:96612400-96623200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr13:96613200-96694200	Weak transcription	A549	lung
11	chr13:96613400-96623200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr13:96613400-96634000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr13:96613400-96641600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:96613400-96643000	Weak transcription	Right Ventricle	heart
15	chr13:96613600-96650000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr13:96613600-96663600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr13:96614000-96652400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr13:96616200-96623000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr13:96616200-96623800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr13:96616200-96668600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr13:96616400-96624200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr13:96616400-96627000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr13:96616400-96636200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr13:96616600-96623400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr13:96616800-96623800	Weak transcription	Liver	Liver
26	chr13:96616800-96624600	Weak transcription	Brain Angular Gyrus	brain
27	chr13:96616800-96628400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr13:96616800-96668400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr13:96617000-96649000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr13:96617000-96663200	Weak transcription	NHDF-Ad	bronchial
31	chr13:96617200-96625200	Weak transcription	Fetal Muscle Leg	muscle
32	chr13:96617400-96638200	Weak transcription	HSMMtube	muscle
33	chr13:96618800-96623800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr13:96618800-96654200	Weak transcription	Fetal Lung	lung
35	chr13:96619000-96622800	Weak transcription	HMEC	breast
36	chr13:96619000-96634200	Weak transcription	Brain Hippocampus Middle	brain
37	chr13:96619600-96638200	Weak transcription	Fetal Intestine Small	intestine
38	chr13:96620200-96623000	Weak transcription	Brain Substantia Nigra	brain
39	chr13:96620600-96622800	Strong transcription	HSMM	muscle
40	chr13:96621000-96623000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr13:96621000-96623400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr13:96621000-96634400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr13:96621000-96636800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr13:96621400-96634200	Weak transcription	Left Ventricle	heart
45	chr13:96621600-96623200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr13:96621600-96668600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr13:96621800-96624400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr13:96621800-96636800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr13:96622000-96637600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr13:96622000-96668600	Weak transcription	Aorta	Aorta

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