Variant report

Variant	rs921510
Chromosome Location	chr15:33117302-33117303
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10519750	0.85[JPT][hapmap]
rs16959182	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16959198	0.92[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16959223	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16959250	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16959442	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1975678	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28575860	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28580622	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56064734	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58349661	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58476108	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58586003	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59044286	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59119474	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs725807	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74011842	0.82[AMR][1000 genomes]
rs74011843	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8039697	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921512	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422296	chr15:32798938-33221215	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv482680	chr15:32958401-33154005	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv832961	chr15:33021177-33134988	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv903977	chr15:33040782-33117302	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv832962	chr15:33111517-33239736	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs921510	HERC2	cis	cerebellum	SCAN
rs921510	TJP1	cis	cerebellum	SCAN
rs921510	TMEM85	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33061200-33141000	Weak transcription	Placenta	Placenta
2	chr15:33096200-33154000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr15:33096400-33159000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:33103800-33139200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:33111200-33130000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:33111600-33118400	Weak transcription	Gastric	stomach
7	chr15:33112000-33126800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:33112000-33130600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:33115800-33118000	Enhancers	HUVEC	blood vessel
10	chr15:33115800-33118600	Enhancers	HSMM	muscle
11	chr15:33116000-33117800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:33116000-33118000	Enhancers	HSMMtube	muscle
13	chr15:33116000-33118600	Flanking Active TSS	A549	lung
14	chr15:33116000-33119200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:33116000-33119200	Enhancers	NHLF	lung
16	chr15:33116200-33117600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:33116200-33117800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:33116400-33117800	Enhancers	HMEC	breast
19	chr15:33116400-33118800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:33116400-33119200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:33116600-33117800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:33116600-33118400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:33116600-33118400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:33116600-33118800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:33116800-33117600	Flanking Active TSS	Osteobl	bone
26	chr15:33116800-33117800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr15:33117000-33117400	Enhancers	Hela-S3	cervix
28	chr15:33117000-33117400	Flanking Active TSS	NHDF-Ad	bronchial
29	chr15:33117000-33117400	Flanking Active TSS	NHEK	skin
30	chr15:33117000-33119400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:33117000-33125600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr15:33117000-33126800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:33117200-33117600	Flanking Active TSS	NH-A	brain
34	chr15:33117200-33117800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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