Variant report

Variant	rs16971734
Chromosome Location	chr15:41562393-41562394
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41554916..41558076-chr15:41560482..41563886,4	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs16952331	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs16971562	0.81[EUR][1000 genomes]
rs16971576	0.83[EUR][1000 genomes]
rs16971647	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16971651	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16971653	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16971654	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16971733	0.93[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs16971735	0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2083238	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2090826	0.85[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2118739	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2412607	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2412610	0.85[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28417774	0.96[ASN][1000 genomes]
rs28468975	0.96[ASN][1000 genomes]
rs28478807	0.89[ASN][1000 genomes]
rs28626792	0.95[ASN][1000 genomes]
rs2899014	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55787465	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55952963	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56262456	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56815966	0.81[EUR][1000 genomes]
rs57009745	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57896923	0.85[EUR][1000 genomes]
rs58060180	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58436082	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58851405	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6492995	0.94[CHD][hapmap]
rs6492996	0.90[ASN][1000 genomes]
rs7165551	0.85[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7166182	0.85[CHB][hapmap];0.87[EUR][1000 genomes]
rs7166581	0.85[AMR][1000 genomes]
rs7167142	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs74012251	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74012252	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74012253	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74012255	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8025660	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8025916	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8029873	0.94[ASN][1000 genomes]
rs8030033	0.88[ASN][1000 genomes]
rs8030683	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8030706	0.85[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8030712	0.84[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8030732	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8030954	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8031542	0.92[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8034073	0.85[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs8034924	0.83[ASN][1000 genomes]
rs8036686	0.85[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs9672272	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9672309	0.83[EUR][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	nsv1045455	chr15:41536624-41620534	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1044438	chr15:41560160-41745480	Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16971734	FAM82A2	cis	parietal	SCAN
rs16971734	MPDU1	trans	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41524200-41563800	Weak transcription	Small Intestine	intestine
2	chr15:41524200-41575800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:41524800-41563800	Weak transcription	Esophagus	oesophagus
4	chr15:41525200-41575400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:41525800-41575200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr15:41536600-41573600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:41537400-41570800	Weak transcription	Ovary	ovary
8	chr15:41537600-41562800	Weak transcription	Lung	lung
9	chr15:41542800-41572000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr15:41543000-41575200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:41545000-41571400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:41549200-41575200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:41550400-41571400	Weak transcription	Right Ventricle	heart
14	chr15:41550400-41575600	Weak transcription	Fetal Brain Male	brain
15	chr15:41550600-41564200	Weak transcription	NHDF-Ad	bronchial
16	chr15:41551800-41568600	Weak transcription	Fetal Lung	lung
17	chr15:41551800-41570600	Weak transcription	HMEC	breast
18	chr15:41552400-41574600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:41552600-41575200	Weak transcription	GM12878-XiMat	blood
20	chr15:41552800-41575800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr15:41553600-41569200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:41554600-41573000	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr15:41554800-41563400	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:41555400-41569000	Weak transcription	Fetal Kidney	kidney
25	chr15:41555400-41570800	Weak transcription	HSMM	muscle
26	chr15:41555600-41564200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:41555600-41566600	Weak transcription	Brain Angular Gyrus	brain
28	chr15:41555600-41569000	Weak transcription	Dnd41	blood
29	chr15:41555600-41570600	Strong transcription	Liver	Liver
30	chr15:41556200-41569000	Weak transcription	K562	blood
31	chr15:41556400-41562800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:41556400-41563800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:41556400-41571600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:41556400-41574400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr15:41556600-41568400	Weak transcription	Stomach Mucosa	stomach
36	chr15:41556600-41568600	Weak transcription	NH-A	brain
37	chr15:41556600-41570800	Weak transcription	Brain Substantia Nigra	brain
38	chr15:41556800-41562400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr15:41556800-41562400	Weak transcription	A549	lung
40	chr15:41556800-41562600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:41556800-41563600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr15:41556800-41563800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr15:41556800-41566200	Weak transcription	Pancreas	Pancrea
44	chr15:41556800-41569200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:41556800-41569600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:41556800-41571600	Weak transcription	Thymus	Thymus
47	chr15:41556800-41571800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr15:41556800-41572600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr15:41556800-41573200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:41556800-41575200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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