Variant report

Variant	rs4773927
Chromosome Location	chr13:96510460-96510461
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	chr13:96506532..96508738-chr13:96509011..96511057,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1596710	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs1807900	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1980942	0.91[ASW][hapmap];0.84[CEU][hapmap];0.84[TSI][hapmap]
rs1996054	0.84[CEU][hapmap]
rs2389530	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3099357	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs3099359	0.90[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3099360	0.91[ASW][hapmap];0.84[CEU][hapmap];0.81[AFR][1000 genomes]
rs3125433	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34482628	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34859372	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4773930	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs509572	0.88[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap]
rs541811	0.81[ASW][hapmap]
rs595696	0.88[CEU][hapmap];0.94[CHB][hapmap]
rs6492820	0.88[CEU][hapmap];0.85[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs7333045	0.84[CEU][hapmap]
rs7983756	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7994626	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7998903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs816139	0.91[ASW][hapmap]
rs9302083	0.85[JPT][hapmap]
rs9516620	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9525085	0.81[ASW][hapmap];0.84[CEU][hapmap];0.84[TSI][hapmap]
rs9525091	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9525095	0.91[ASW][hapmap];0.84[CEU][hapmap];0.84[TSI][hapmap]
rs9561930	0.87[JPT][hapmap]
rs9561949	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4773927	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL
rs4773927	DZIP1	cis	parietal	SCAN
rs4773927	UGGT2	cis	Muscle Skeletal	GTEx

Chromatin state (count:85 , 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	chr13:96499400-96515400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr13:96502000-96522400	Weak transcription	Colon Smooth Muscle	Colon
6	chr13:96502400-96535400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr13:96502600-96552600	Weak transcription	Brain Germinal Matrix	brain
8	chr13:96502800-96514800	Weak transcription	Gastric	stomach
9	chr13:96502800-96562600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr13:96503000-96510600	Weak transcription	NHLF	lung
11	chr13:96503000-96517400	Weak transcription	K562	blood
12	chr13:96503000-96522600	Weak transcription	Aorta	Aorta
13	chr13:96503000-96522600	Weak transcription	Pancreas	Pancrea
14	chr13:96503000-96523600	Weak transcription	Esophagus	oesophagus
15	chr13:96503000-96526800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr13:96503000-96527200	Weak transcription	Fetal Kidney	kidney
17	chr13:96503000-96567400	Weak transcription	NHEK	skin
18	chr13:96503200-96522600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr13:96503200-96522800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr13:96503200-96527800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr13:96503200-96535200	Weak transcription	HepG2	liver
22	chr13:96503200-96542000	Weak transcription	Brain Substantia Nigra	brain
23	chr13:96503200-96542000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr13:96503200-96542200	Weak transcription	Brain Hippocampus Middle	brain
25	chr13:96503200-96558000	Weak transcription	NHDF-Ad	bronchial
26	chr13:96503200-96558200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr13:96503200-96558800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr13:96503400-96520400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr13:96503400-96521800	Weak transcription	HSMMtube	muscle
30	chr13:96503400-96522600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr13:96503400-96528600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr13:96503400-96542000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr13:96503400-96555400	Weak transcription	Fetal Heart	heart
34	chr13:96503400-96580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr13:96503600-96510600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr13:96503600-96510600	Weak transcription	Stomach Mucosa	stomach
37	chr13:96503600-96510800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr13:96503600-96528600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr13:96503600-96528600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr13:96503600-96559000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr13:96503600-96562800	Weak transcription	Fetal Brain Female	brain
42	chr13:96503800-96510600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr13:96503800-96510800	Weak transcription	Osteobl	bone
44	chr13:96503800-96513400	Weak transcription	Fetal Stomach	stomach
45	chr13:96503800-96522600	Weak transcription	Left Ventricle	heart
46	chr13:96503800-96522800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr13:96503800-96526800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr13:96503800-96548200	Weak transcription	A549	lung
49	chr13:96504000-96510600	Weak transcription	NH-A	brain
50	chr13:96504000-96510800	Weak transcription	Muscle Satellite Cultured Cells	--

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