Variant report

Variant	rs11073221
Chromosome Location	chr15:30020106-30020107
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	POLR2A	chr15:30020039-30020882	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
HMGN2P5	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10519663	0.91[ASN][1000 genomes]
rs10852002	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11073185	0.91[ASN][1000 genomes]
rs11073187	0.91[ASN][1000 genomes]
rs11073270	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11073279	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12438685	0.91[ASN][1000 genomes]
rs12440088	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17683205	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293186	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[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];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28376883	0.80[EUR][1000 genomes]
rs28831790	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3784355	1.00[JPT][hapmap]
rs59865887	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9806607	0.89[YRI][hapmap]
rs9920553	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9920621	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9972620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv832944	chr15:29861062-30082057	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv832945	chr15:29932599-30123721	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	esv2422463	chr15:30003189-30215336	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:29989600-30021200	Strong transcription	Duodenum Smooth Muscle	Duodenum
2	chr15:29989600-30027200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr15:29990200-30028400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:29990400-30026400	Strong transcription	Stomach Smooth Muscle	stomach
5	chr15:29991200-30020200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:29991200-30022400	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr15:29992000-30026600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:29996200-30021400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:30005000-30023000	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr15:30005400-30022800	Strong transcription	HSMMtube	muscle
11	chr15:30007200-30021400	Strong transcription	Fetal Kidney	kidney
12	chr15:30007200-30021400	Strong transcription	NHLF	lung
13	chr15:30014800-30021200	Strong transcription	HMEC	breast
14	chr15:30014800-30028400	Strong transcription	NHEK	skin
15	chr15:30015000-30021600	Strong transcription	Brain Angular Gyrus	brain
16	chr15:30015000-30022200	Strong transcription	Osteobl	bone
17	chr15:30015000-30024400	Weak transcription	Psoas Muscle	Psoas
18	chr15:30015000-30028400	Weak transcription	Stomach Mucosa	stomach
19	chr15:30015000-30035000	Strong transcription	Adipose Nuclei	Adipose
20	chr15:30015200-30020800	Strong transcription	Brain Anterior Caudate	brain
21	chr15:30015200-30021200	Strong transcription	Brain Hippocampus Middle	brain
22	chr15:30015200-30021400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:30015200-30021400	Strong transcription	Duodenum Mucosa	Duodenum
24	chr15:30015200-30021600	Strong transcription	Ovary	ovary
25	chr15:30015200-30022800	Strong transcription	NH-A	brain
26	chr15:30015200-30023200	Strong transcription	Placenta	Placenta
27	chr15:30015200-30024200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:30015400-30026600	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr15:30015400-30028600	Strong transcription	HUVEC	blood vessel
30	chr15:30015600-30021000	Strong transcription	NHDF-Ad	bronchial
31	chr15:30015600-30021400	Strong transcription	Fetal Lung	lung
32	chr15:30015600-30026600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:30015600-30034800	Strong transcription	Fetal Muscle Leg	muscle
34	chr15:30015600-30035200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr15:30015600-30037600	Weak transcription	Small Intestine	intestine
36	chr15:30015800-30023000	Strong transcription	Fetal Stomach	stomach
37	chr15:30015800-30023200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:30015800-30026400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr15:30015800-30026800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr15:30015800-30027200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr15:30015800-30027600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:30015800-30034400	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:30016400-30020400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr15:30016400-30021000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:30016600-30020200	Strong transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr15:30016600-30021400	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr15:30016600-30021400	Strong transcription	HSMM	muscle
48	chr15:30016600-30021800	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr15:30016600-30023000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:30016600-30025800	Strong transcription	Left Ventricle	heart

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