Variant report

Variant	rs9516621
Chromosome Location	chr13:96546377-96546378
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10508027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs11616953	0.83[EUR][1000 genomes]
rs11618108	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs11619636	0.81[ASN][1000 genomes]
rs12428062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12430152	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1330556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330557	0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs16951334	0.82[CHD][hapmap];0.93[MEX][hapmap]
rs16951448	0.81[ASN][1000 genomes]
rs1788062	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1854758	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]
rs2170813	1.00[CEU][hapmap]
rs3099362	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099363	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3101570	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4254181	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4347496	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4383020	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4409947	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4526890	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4547219	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs476954	0.85[AFR][1000 genomes]
rs4773932	0.81[ASN][1000 genomes]
rs531549	0.81[ASN][1000 genomes]
rs534429	0.88[CEU][hapmap]
rs537463	0.81[ASN][1000 genomes]
rs540213	0.88[CEU][hapmap]
rs56077337	0.81[ASN][1000 genomes]
rs565297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs565851	0.88[CEU][hapmap]
rs565898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs661544	0.81[ASN][1000 genomes]
rs662884	0.88[CEU][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs674565	0.88[CEU][hapmap]
rs72636541	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72636556	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72636562	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72636570	0.95[ASN][1000 genomes]
rs7323408	1.00[JPT][hapmap]
rs7331211	1.00[JPT][hapmap]
rs7331549	1.00[JPT][hapmap]
rs7332078	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7334320	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7335209	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7339059	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7999737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs8000018	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs816142	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]
rs9525077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9525079	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9525097	0.81[AFR][1000 genomes]
rs9584324	1.00[JPT][hapmap]
rs9590344	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9516621	UGGT2	cis	cerebellum	SCAN
rs9516621	DZIP1	cis	Artery Tibial	GTEx
rs9516621	UGCGL2	cis	multi-tissue	Pritchard
rs9516621	DZIP1	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96478000-96568400	Weak transcription	Placenta	Placenta
2	chr13:96495000-96590800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:96498400-96549800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:96502600-96552600	Weak transcription	Brain Germinal Matrix	brain
5	chr13:96502800-96562600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr13:96503000-96567400	Weak transcription	NHEK	skin
7	chr13:96503200-96558000	Weak transcription	NHDF-Ad	bronchial
8	chr13:96503200-96558200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:96503200-96558800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr13:96503400-96555400	Weak transcription	Fetal Heart	heart
11	chr13:96503400-96580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr13:96503600-96559000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr13:96503600-96562800	Weak transcription	Fetal Brain Female	brain
14	chr13:96503800-96548200	Weak transcription	A549	lung
15	chr13:96506600-96554800	Weak transcription	GM12878-XiMat	blood
16	chr13:96510800-96556000	Weak transcription	Psoas Muscle	Psoas
17	chr13:96511000-96559000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr13:96511000-96559200	Weak transcription	Spleen	Spleen
19	chr13:96515000-96553400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr13:96518200-96553200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr13:96519600-96546400	Weak transcription	Right Ventricle	heart
22	chr13:96520800-96559200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr13:96523000-96559000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr13:96523200-96547800	Weak transcription	Colon Smooth Muscle	Colon
25	chr13:96523200-96581800	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr13:96524000-96561200	Weak transcription	HMEC	breast
27	chr13:96524200-96560400	Weak transcription	Brain Angular Gyrus	brain
28	chr13:96526400-96548200	Weak transcription	K562	blood
29	chr13:96527800-96559200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr13:96528200-96548200	Weak transcription	HUVEC	blood vessel
31	chr13:96528200-96558600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr13:96528800-96559000	Weak transcription	Ovary	ovary
33	chr13:96529000-96550200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr13:96529200-96552600	Weak transcription	NHLF	lung
35	chr13:96529200-96558000	Weak transcription	Fetal Kidney	kidney
36	chr13:96529400-96547600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr13:96529400-96558200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr13:96529400-96559000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr13:96529400-96559000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr13:96529400-96559000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr13:96529400-96559200	Weak transcription	Esophagus	oesophagus
42	chr13:96529600-96559000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr13:96529600-96559000	Weak transcription	Fetal Stomach	stomach
44	chr13:96534000-96547000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr13:96534600-96559000	Weak transcription	Pancreas	Pancrea
46	chr13:96535000-96559200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr13:96535800-96555800	Weak transcription	HepG2	liver
48	chr13:96536000-96546800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr13:96536200-96559000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr13:96536200-96559000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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