Variant report

Variant	rs16970216
Chromosome Location	chr15:79192416-79192417
allele	A/C
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	chr15:79191641-79192479	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr15:79192244-79192464	HepG2	liver:	n/a	n/a
3	POLR2A	chr15:79192009-79192416	GM12892	blood:	n/a	n/a
4	POLR2A	chr15:79190091-79192514	K562	blood:	n/a	n/a
5	POLR2A	chr15:79191798-79200534	HepG2	liver:	n/a	n/a
6	POLR2A	chr15:79191799-79200567	A549	lung:	n/a	n/a
7	POLR2A	chr15:79191979-79192643	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:79190765-79192441	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:79191779-79200429	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:79164137..79170280-chr15:79189650..79200289,14	K562	blood:
2	chr15:79166781..79169247-chr15:79192371..79193935,2	K562	blood:

Variant related genes	Relation type
RNU6-415P	TF binding region
ENSG00000185787	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10519214	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1075965	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16970190	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16970207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16970215	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16970248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16970350	0.91[MEX][hapmap]
rs1808757	0.80[AMR][1000 genomes]
rs3803545	1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3825930	0.85[AMR][1000 genomes]
rs4778627	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4778645	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4778659	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4778858	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4778952	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4779081	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4779082	1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56963875	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58105551	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58257692	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58807257	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59238093	0.85[AMR][1000 genomes]
rs60009001	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61009187	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61504829	0.85[AMR][1000 genomes]
rs7171615	0.94[ASN][1000 genomes]
rs73470371	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73470375	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73470383	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7402463	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7402487	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs894785	0.92[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv522996	chr15:79175813-79192416	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16970216	CTSH	cis	lymphoblastoid	seeQTL
rs16970216	CTSH	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79170400-79198600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:79171200-79199600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:79171200-79199800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr15:79171200-79215600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:79171600-79199600	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr15:79171600-79200400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr15:79171800-79207800	Strong transcription	Fetal Thymus	thymus
8	chr15:79172000-79200200	Strong transcription	HUVEC	blood vessel
9	chr15:79172000-79202800	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr15:79172200-79197600	Strong transcription	Placenta	Placenta
11	chr15:79172200-79199600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:79172200-79200200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr15:79172200-79207000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr15:79172400-79200000	Strong transcription	Fetal Intestine Large	intestine
15	chr15:79172400-79216200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:79172600-79201800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr15:79172600-79207400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:79172800-79197800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:79172800-79199800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:79172800-79199800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:79172800-79202600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:79172800-79205400	Strong transcription	Fetal Lung	lung
23	chr15:79172800-79206800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:79173000-79197400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:79173200-79194400	Strong transcription	NH-A	brain
26	chr15:79173200-79199600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:79173400-79203000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:79173600-79206200	Strong transcription	Fetal Muscle Leg	muscle
29	chr15:79173600-79206400	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr15:79173800-79206400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr15:79174000-79199200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:79174200-79194400	Strong transcription	NHDF-Ad	bronchial
33	chr15:79174600-79194200	Strong transcription	HSMM	muscle
34	chr15:79175200-79194000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:79175200-79194000	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr15:79175200-79198000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:79175400-79193600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr15:79176400-79199800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr15:79176600-79202400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr15:79176800-79215200	Strong transcription	Dnd41	blood
41	chr15:79177000-79202200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:79177000-79207800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr15:79177200-79197400	Strong transcription	HMEC	breast
44	chr15:79177200-79198000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:79177200-79206800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr15:79177800-79196400	Strong transcription	A549	lung
47	chr15:79178000-79194000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:79178000-79200000	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr15:79178000-79200400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:79178200-79197400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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