Variant report

Variant	rs16970190
Chromosome Location	chr15:79177669-79177670
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:79164165..79169196-chr15:79177186..79180776,6	MCF-7	breast:
2	chr15:79168424..79170756-chr15:79176616..79179501,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185787	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10519214	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1075965	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16970207	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16970215	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16970216	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16970248	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1808757	0.80[AMR][1000 genomes]
rs3803545	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3825930	0.85[AMR][1000 genomes]
rs4778627	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4778645	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4778659	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4778858	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4778952	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4779081	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4779082	1.00[CHB][hapmap];0.83[JPT][hapmap];0.97[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56963875	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58105551	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58257692	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58807257	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58858460	0.84[ASN][1000 genomes]
rs59238093	0.85[AMR][1000 genomes]
rs60009001	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61009187	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61504829	0.85[AMR][1000 genomes]
rs6495342	0.84[ASN][1000 genomes]
rs7171615	1.00[ASN][1000 genomes]
rs73470371	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73470375	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73470383	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7402463	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7402487	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16970190	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	chr15:79167000-79179200	Weak transcription	Esophagus	oesophagus
2	chr15:79167200-79178200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:79167800-79183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:79169800-79180000	Weak transcription	Gastric	stomach
5	chr15:79170200-79187000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:79170400-79198600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:79170600-79182400	Weak transcription	Aorta	Aorta
8	chr15:79170600-79183200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:79170800-79178200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr15:79170800-79192400	Weak transcription	Stomach Mucosa	stomach
11	chr15:79171000-79179000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:79171200-79199600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr15:79171200-79199800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:79171200-79215600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:79171600-79180400	Weak transcription	Small Intestine	intestine
16	chr15:79171600-79199600	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr15:79171600-79200400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr15:79171800-79178000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
19	chr15:79171800-79207800	Strong transcription	Fetal Thymus	thymus
20	chr15:79172000-79178600	Weak transcription	Spleen	Spleen
21	chr15:79172000-79185200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr15:79172000-79200200	Strong transcription	HUVEC	blood vessel
23	chr15:79172000-79202800	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr15:79172200-79179600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:79172200-79197600	Strong transcription	Placenta	Placenta
26	chr15:79172200-79199600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:79172200-79200200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr15:79172200-79207000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr15:79172400-79200000	Strong transcription	Fetal Intestine Large	intestine
30	chr15:79172400-79216200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:79172600-79182400	Strong transcription	Primary B cells from cord blood	blood
32	chr15:79172600-79201800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr15:79172600-79207400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:79172800-79178600	Weak transcription	Right Ventricle	heart
35	chr15:79172800-79197800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:79172800-79199800	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:79172800-79199800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr15:79172800-79202600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:79172800-79205400	Strong transcription	Fetal Lung	lung
40	chr15:79172800-79206800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:79173000-79197400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr15:79173200-79194400	Strong transcription	NH-A	brain
43	chr15:79173200-79199600	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr15:79173400-79203000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr15:79173600-79180800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr15:79173600-79206200	Strong transcription	Fetal Muscle Leg	muscle
47	chr15:79173600-79206400	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr15:79173800-79182200	Strong transcription	Primary hematopoietic stem cells	blood
49	chr15:79173800-79206400	Strong transcription	Fetal Muscle Trunk	muscle
50	chr15:79174000-79185800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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