Variant report

Variant	rs11646019
Chromosome Location	chr16:82817006-82817007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11640600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11642248	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11643292	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12386028	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12919538	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17191840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17192123	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17192152	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17276586	0.91[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17277145	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1903617	0.81[ASN][1000 genomes]
rs4783270	0.82[ASN][1000 genomes]
rs57519947	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59217991	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61037133	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62034546	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62034548	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72805944	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8043851	0.87[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8060885	0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532599	chr16:82074439-82926863	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	nsv573367	chr16:82140561-83040846	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1057341	chr16:82363800-83198907	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
4	nsv542997	chr16:82363800-83198907	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv573379	chr16:82713551-82887631	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	esv2751616	chr16:82714696-82852296	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1067216	chr16:82719694-82821762	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
8	nsv543000	chr16:82719694-82821762	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1066132	chr16:82769526-82847359	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv543001	chr16:82769526-82847359	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1063617	chr16:82786803-83229529	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1063412	chr16:82806653-82826507	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv431523	chr16:82817006-82824214	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11646019	BCMO1	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:82805600-82821600	Weak transcription	NHEK	skin
2	chr16:82807200-82817800	Weak transcription	HMEC	breast
3	chr16:82808000-82824800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr16:82810600-82834800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr16:82810800-82821400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr16:82812000-82821600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr16:82812800-82817200	Enhancers	Psoas Muscle	Psoas
8	chr16:82813000-82817400	Enhancers	Right Ventricle	heart
9	chr16:82813800-82819600	Enhancers	Fetal Muscle Leg	muscle
10	chr16:82814400-82819800	Enhancers	Primary B cells from peripheral blood	blood
11	chr16:82815000-82817200	Enhancers	Colon Smooth Muscle	Colon
12	chr16:82815200-82817400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr16:82815400-82817400	Enhancers	Fetal Intestine Small	intestine
14	chr16:82815600-82817200	Enhancers	H1 Cell Line	embryonic stem cell
15	chr16:82815600-82817200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr16:82815600-82817200	Enhancers	Left Ventricle	heart
17	chr16:82815600-82817200	Enhancers	Right Atrium	heart
18	chr16:82815600-82817200	Enhancers	HSMM	muscle
19	chr16:82815800-82817200	Enhancers	Fetal Muscle Trunk	muscle
20	chr16:82815800-82821800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr16:82815800-82834600	Weak transcription	HUVEC	blood vessel
22	chr16:82816000-82817800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr16:82816000-82818000	Weak transcription	Colonic Mucosa	Colon
24	chr16:82816200-82817200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr16:82816200-82817200	Enhancers	Fetal Stomach	stomach
26	chr16:82816200-82817200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr16:82816200-82817400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr16:82816400-82817200	Enhancers	Fetal Intestine Large	intestine
29	chr16:82816400-82817200	Enhancers	Gastric	stomach
30	chr16:82816400-82817200	Enhancers	Pancreas	Pancrea
31	chr16:82816400-82818000	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr16:82816400-82818000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr16:82816600-82817400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr16:82816600-82818600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr16:82816800-82817200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr16:82816800-82817200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr16:82816800-82817400	Enhancers	Brain Angular Gyrus	brain
38	chr16:82816800-82817800	Weak transcription	Spleen	Spleen
39	chr16:82817000-82817200	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr16:82817000-82817200	Active TSS	Rectal Smooth Muscle	rectum
41	chr16:82817000-82817200	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr16:82817000-82817200	Enhancers	Stomach Smooth Muscle	stomach
43	chr16:82817000-82817400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr16:82817000-82818000	Weak transcription	Aorta	Aorta
45	chr16:82817000-82818000	Weak transcription	Brain Germinal Matrix	brain
46	chr16:82817000-82818200	Enhancers	Duodenum Mucosa	Duodenum
47	chr16:82817000-82819000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr16:82817000-82821600	Weak transcription	HSMMtube	muscle

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