Variant report

Variant	rs1541965
Chromosome Location	chr15:79205126-79205127
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:79204974..79207838-chr15:79210921..79213668,2	K562	blood:
2	chr15:79196785..79198846-chr15:79204561..79206760,2	K562	blood:
3	chr15:79204348..79206445-chr15:79222058..79224035,2	MCF-7	breast:
4	chr15:79203581..79205998-chr15:79208517..79210906,2	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs16970187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16970254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289692	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5029904	0.80[JPT][hapmap]
rs5849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7166405	0.88[GIH][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1541965	CTSH	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79171200-79215600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:79171800-79207800	Strong transcription	Fetal Thymus	thymus
3	chr15:79172200-79207000	Strong transcription	Primary B cells from peripheral blood	blood
4	chr15:79172400-79216200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:79172600-79207400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:79172800-79205400	Strong transcription	Fetal Lung	lung
7	chr15:79172800-79206800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:79173600-79206200	Strong transcription	Fetal Muscle Leg	muscle
9	chr15:79173600-79206400	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr15:79173800-79206400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr15:79176800-79215200	Strong transcription	Dnd41	blood
12	chr15:79177000-79207800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr15:79177200-79206800	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr15:79178200-79219400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr15:79185600-79208600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:79187400-79213600	Weak transcription	Small Intestine	intestine
17	chr15:79188000-79209400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr15:79190000-79208200	Strong transcription	Primary T cells from cord blood	blood
19	chr15:79190000-79222200	Strong transcription	Thymus	Thymus
20	chr15:79190400-79207000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:79190400-79208200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:79194800-79207000	Strong transcription	K562	blood
23	chr15:79197200-79213600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr15:79199000-79206200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:79199000-79206400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:79199000-79213800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr15:79199200-79205200	Weak transcription	Right Atrium	heart
28	chr15:79199200-79207600	Strong transcription	Placenta	Placenta
29	chr15:79199400-79205400	Strong transcription	HMEC	breast
30	chr15:79199400-79206400	Weak transcription	Psoas Muscle	Psoas
31	chr15:79199600-79206200	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr15:79199600-79206600	Strong transcription	Osteobl	bone
33	chr15:79199600-79207800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:79199600-79218800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:79199800-79208000	Strong transcription	A549	lung
36	chr15:79199800-79229400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:79200000-79206400	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:79200200-79205200	Weak transcription	Right Ventricle	heart
39	chr15:79200200-79206400	Weak transcription	Left Ventricle	heart
40	chr15:79200400-79205400	Strong transcription	NHDF-Ad	bronchial
41	chr15:79200400-79205800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr15:79200400-79205800	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr15:79200400-79208200	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:79200800-79206400	Strong transcription	Lung	lung
45	chr15:79200800-79207200	Strong transcription	Primary B cells from cord blood	blood
46	chr15:79200800-79208200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr15:79200800-79208200	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr15:79200800-79208400	Strong transcription	Primary hematopoietic stem cells	blood
49	chr15:79200800-79208400	Strong transcription	Fetal Intestine Large	intestine
50	chr15:79201000-79205400	Strong transcription	HSMMtube	muscle

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