Variant report

Variant	rs11645180
Chromosome Location	chr16:75613074-75613075
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75604944..75610027-chr16:75610996..75613985,4	K562	blood:
2	chr16:75606093..75608487-chr16:75610789..75613227,2	MCF-7	breast:
3	chr16:75602536..75605291-chr16:75611992..75614146,2	MCF-7	breast:
4	chr16:75611305..75613480-chr16:75615216..75617290,3	K562	blood:
5	chr16:75549824..75551529-chr16:75610476..75613166,2	MCF-7	breast:
6	chr16:75612046..75614181-chr16:75618703..75620735,2	K562	blood:
7	chr16:75601777..75604413-chr16:75611390..75613643,2	K562	blood:

Variant related genes	Relation type
ENSG00000262583	Chromatin interaction
ENSG00000034713	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11149840	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11149841	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11641024	0.83[AFR][1000 genomes]
rs11642599	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11642713	0.83[AFR][1000 genomes]
rs11644468	0.81[EUR][1000 genomes]
rs11648478	0.87[YRI][hapmap]
rs11649388	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12149103	0.93[CEU][hapmap]
rs3743602	0.81[AMR][1000 genomes]
rs3743604	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3784932	1.00[CEU][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3826107	0.93[CEU][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs4149500	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4149501	1.00[CEU][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4149504	1.00[CEU][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4485400	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59359930	0.85[EUR][1000 genomes]
rs60988480	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7202717	1.00[CEU][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7206481	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74024804	0.84[EUR][1000 genomes]
rs8046531	0.84[ASW][hapmap];0.93[CEU][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs8046977	0.85[EUR][1000 genomes]
rs8048818	1.00[CEU][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv525955	chr16:75473332-75628345	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
5	nsv532561	chr16:75519574-75636977	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11645180	ADAT1	cis	Muscle Skeletal	GTEx
rs11645180	ADAT1	cis	Nerve Tibial	GTEx
rs11645180	ADAT1	cis	cerebellum	SCAN
rs11645180	VAC14	cis	cerebellum	SCAN
rs11645180	ADAT1	cis	parietal	SCAN
rs11645180	ADAT1	cis	Esophagus Muscularis	GTEx
rs11645180	ADAT1	Cis_1M	lymphoblastoid	RTeQTL
rs11645180	ADAT1	cis	Skin Sun Exposed Lower leg	GTEx
rs11645180	ADAT1	cis	Adipose Subcutaneous	GTEx
rs11645180	ADAT1	cis	lung	GTEx
rs11645180	ADAT1	cis	multi-tissue	Pritchard
rs11645180	ADAT1	cis	Thyroid	GTEx
rs11645180	ADAT1	cis	Artery Tibial	GTEx
rs11645180	CHST4	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75601200-75624400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:75601600-75613400	Strong transcription	NH-A	brain
3	chr16:75601600-75613800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr16:75601600-75613800	Strong transcription	A549	lung
5	chr16:75601600-75614400	Genic enhancers	Brain Anterior Caudate	brain
6	chr16:75601600-75615200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr16:75601600-75615400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr16:75601800-75614400	Strong transcription	Thymus	Thymus
9	chr16:75601800-75615400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr16:75602000-75613200	Strong transcription	HepG2	liver
11	chr16:75602000-75613200	Strong transcription	NHLF	lung
12	chr16:75602000-75613600	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr16:75602000-75614000	Strong transcription	Fetal Lung	lung
14	chr16:75602000-75614200	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr16:75602000-75614200	Strong transcription	Osteobl	bone
16	chr16:75602000-75614400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr16:75602000-75614600	Strong transcription	Placenta	Placenta
18	chr16:75602000-75615000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr16:75602000-75615200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr16:75602200-75614400	Strong transcription	Fetal Intestine Large	intestine
21	chr16:75602200-75614800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr16:75602600-75614200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr16:75602600-75614400	Strong transcription	Fetal Brain Female	brain
24	chr16:75602800-75613800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr16:75602800-75614400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr16:75602800-75615400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr16:75603000-75614800	Strong transcription	Primary T cells from cord blood	blood
28	chr16:75603400-75614400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr16:75603400-75614600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr16:75603400-75615000	Strong transcription	Dnd41	blood
31	chr16:75603800-75613600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr16:75604000-75615400	Strong transcription	Fetal Stomach	stomach
33	chr16:75604200-75614400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr16:75604200-75622600	Weak transcription	Right Atrium	heart
35	chr16:75604400-75614600	Strong transcription	Fetal Muscle Leg	muscle
36	chr16:75605200-75613800	Strong transcription	Primary B cells from cord blood	blood
37	chr16:75605200-75614000	Strong transcription	Lung	lung
38	chr16:75605400-75614200	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr16:75605400-75615400	Strong transcription	Fetal Thymus	thymus
40	chr16:75605400-75616000	Strong transcription	Fetal Intestine Small	intestine
41	chr16:75606400-75615200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr16:75606800-75614200	Strong transcription	Adipose Nuclei	Adipose
43	chr16:75607000-75614400	Strong transcription	Liver	Liver
44	chr16:75607000-75623200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr16:75607200-75615200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr16:75607400-75614400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr16:75607400-75614600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr16:75607600-75613400	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr16:75607600-75614400	Strong transcription	Duodenum Mucosa	Duodenum
50	chr16:75607600-75614400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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