Variant report

Variant	rs2389530
Chromosome Location	chr13:96550754-96550755
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr13:96550671-96550815	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr13:96550653-96550774	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96548750..96552218-chr13:96554707..96557243,3	K562	blood:
2	chr13:96548785..96550762-chr13:96554235..96556207,2	K562	blood:

Variant related genes	Relation type
UGGT2	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12583795	0.81[CHB][hapmap]
rs12583796	0.81[CHB][hapmap]
rs1596710	0.87[EUR][1000 genomes]
rs1807900	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1980942	0.88[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs1996054	0.88[CEU][hapmap]
rs2389531	0.87[EUR][1000 genomes]
rs2774113	0.80[CEU][hapmap]
rs3099357	1.00[ASW][hapmap];0.84[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs3099359	0.84[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3099360	0.81[CEU][hapmap]
rs3125433	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34482628	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34859372	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3901894	0.81[CHB][hapmap]
rs4773927	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]
rs4773930	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs481927	0.81[EUR][1000 genomes]
rs489179	0.82[EUR][1000 genomes]
rs509572	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs511029	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs521235	0.80[CEU][hapmap]
rs527096	1.00[AFR][1000 genomes]
rs527680	0.80[CEU][hapmap]
rs541811	0.80[CEU][hapmap]
rs544080	0.83[CEU][hapmap]
rs555221	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs576184	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs595696	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6492820	1.00[ASW][hapmap];0.84[CEU][hapmap];0.90[CHB][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs6492821	0.81[CHB][hapmap]
rs6492826	0.80[CEU][hapmap]
rs7333045	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs7334552	0.81[CHB][hapmap]
rs7338266	0.81[CHB][hapmap]
rs7983756	0.80[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap]
rs7994626	0.92[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7998903	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816139	0.80[TSI][hapmap]
rs9302083	0.93[JPT][hapmap]
rs9516620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516629	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9525081	0.80[EUR][1000 genomes]
rs9525085	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs9525086	0.82[EUR][1000 genomes]
rs9525091	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9525095	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs9525098	0.81[CEU][hapmap]
rs9561939	0.80[CHB][hapmap]
rs9561949	0.85[EUR][1000 genomes]
rs9742440	0.82[EUR][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2389530	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL
rs2389530	UGGT2	cis	Muscle Skeletal	GTEx
rs2389530	DZIP1	cis	parietal	SCAN

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	chr13:96502600-96552600	Weak transcription	Brain Germinal Matrix	brain
4	chr13:96502800-96562600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr13:96503000-96567400	Weak transcription	NHEK	skin
6	chr13:96503200-96558000	Weak transcription	NHDF-Ad	bronchial
7	chr13:96503200-96558200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:96503200-96558800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr13:96503400-96555400	Weak transcription	Fetal Heart	heart
10	chr13:96503400-96580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:96503600-96559000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr13:96503600-96562800	Weak transcription	Fetal Brain Female	brain
13	chr13:96506600-96554800	Weak transcription	GM12878-XiMat	blood
14	chr13:96510800-96556000	Weak transcription	Psoas Muscle	Psoas
15	chr13:96511000-96559000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr13:96511000-96559200	Weak transcription	Spleen	Spleen
17	chr13:96515000-96553400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr13:96518200-96553200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr13:96520800-96559200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr13:96523000-96559000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr13:96523200-96581800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr13:96524000-96561200	Weak transcription	HMEC	breast
23	chr13:96524200-96560400	Weak transcription	Brain Angular Gyrus	brain
24	chr13:96527800-96559200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr13:96528200-96558600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr13:96528800-96559000	Weak transcription	Ovary	ovary
27	chr13:96529200-96552600	Weak transcription	NHLF	lung
28	chr13:96529200-96558000	Weak transcription	Fetal Kidney	kidney
29	chr13:96529400-96558200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr13:96529400-96559000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr13:96529400-96559000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr13:96529400-96559000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr13:96529400-96559200	Weak transcription	Esophagus	oesophagus
34	chr13:96529600-96559000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr13:96529600-96559000	Weak transcription	Fetal Stomach	stomach
36	chr13:96534600-96559000	Weak transcription	Pancreas	Pancrea
37	chr13:96535000-96559200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr13:96535800-96555800	Weak transcription	HepG2	liver
39	chr13:96536200-96559000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr13:96536200-96559000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr13:96536200-96587200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr13:96537000-96558000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr13:96537800-96558200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr13:96538000-96559000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr13:96539400-96561200	Weak transcription	NH-A	brain
46	chr13:96540400-96557800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr13:96542400-96576800	Weak transcription	HSMMtube	muscle
48	chr13:96542400-96581600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr13:96542800-96559000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr13:96542800-96559000	Weak transcription	Gastric	stomach

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