Variant report

Variant	rs554882
Chromosome Location	chr13:110917782-110917783
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL4A2-AS2-2	chr13:110917598-110918460	NONHSAT035141

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1193069	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1193070	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2847468	0.88[ASN][1000 genomes]
rs476241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs497888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs540519	0.80[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs572713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs627603	0.84[ASN][1000 genomes]
rs641314	0.82[ASN][1000 genomes]
rs6492252	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs669398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs671633	0.83[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs680860	0.80[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs681777	0.80[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs686642	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs903351	0.91[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052147	chr13:110765635-110917782	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:110901000-110919400	Weak transcription	Fetal Brain Male	brain
2	chr13:110904200-110918200	Weak transcription	Pancreas	Pancrea
3	chr13:110909200-110917800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr13:110911200-110924000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr13:110911800-110918800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr13:110912200-110924000	Enhancers	Left Ventricle	heart
7	chr13:110912400-110917800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr13:110912400-110919600	Enhancers	NHDF-Ad	bronchial
9	chr13:110913400-110920200	Enhancers	Fetal Heart	heart
10	chr13:110914000-110917800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr13:110914000-110917800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr13:110914000-110917800	Enhancers	Fetal Stomach	stomach
13	chr13:110914000-110918000	Enhancers	Ovary	ovary
14	chr13:110914000-110918400	Enhancers	Lung	lung
15	chr13:110914000-110922600	Enhancers	Right Atrium	heart
16	chr13:110914200-110918200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr13:110914600-110917800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr13:110914800-110918400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr13:110914800-110919400	Weak transcription	Esophagus	oesophagus
20	chr13:110915200-110918600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr13:110915200-110920000	Enhancers	HUVEC	blood vessel
22	chr13:110915200-110936200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr13:110915400-110918400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr13:110915400-110919400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr13:110915400-110919800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr13:110915400-110920000	Enhancers	Colon Smooth Muscle	Colon
27	chr13:110915600-110918400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr13:110915600-110918600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr13:110915600-110919000	Enhancers	NHLF	lung
30	chr13:110915600-110935800	Weak transcription	Gastric	stomach
31	chr13:110916200-110918400	Enhancers	NHEK	skin
32	chr13:110916200-110918800	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr13:110916200-110921400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr13:110916400-110918000	Enhancers	Fetal Kidney	kidney
35	chr13:110916400-110918200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr13:110916400-110918600	Genic enhancers	Right Ventricle	heart
37	chr13:110916400-110918800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr13:110916400-110919400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr13:110916400-110919800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr13:110916400-110919800	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr13:110916400-110919800	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr13:110916400-110921000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr13:110916400-110921400	Enhancers	H1 Cell Line	embryonic stem cell
44	chr13:110916400-110921400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr13:110916400-110921400	Enhancers	Spleen	Spleen
46	chr13:110916600-110918200	Weak transcription	Aorta	Aorta
47	chr13:110916600-110918600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr13:110916600-110919600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr13:110916600-110920200	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr13:110916600-110922200	Weak transcription	HSMM	muscle

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