Variant report

Variant	rs1036938
Chromosome Location	chr15:79237247-79237248
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:79164120..79166260-chr15:79235714..79238649,3	K562	blood:
2	chr15:79228914..79232769-chr15:79235901..79239047,4	MCF-7	breast:
3	chr15:79222345..79225252-chr15:79235201..79237549,2	K562	blood:
4	chr15:79164120..79166028-chr15:79235714..79238649,2	K562	blood:
5	chr15:79224751..79228848-chr15:79235939..79238870,4	MCF-7	breast:
6	chr15:79219205..79223895-chr15:79234790..79239038,6	MCF-7	breast:
7	chr15:79229734..79233307-chr15:79235000..79238757,6	MCF-7	breast:
8	chr15:79228459..79231609-chr15:79232688..79237314,4	K562	blood:
9	chr15:79223240..79225058-chr15:79235224..79237418,3	MCF-7	breast:
10	chr15:79228950..79233188-chr15:79235013..79237607,6	K562	blood:
11	chr15:79236829..79239228-chr15:79240562..79242151,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000185787	Chromatin interaction
ENSG00000103811	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10152587	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152589	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036937	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036939	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10400877	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10400881	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10400902	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs11072815	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072817	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855406	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11856301	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913968	0.89[EUR][1000 genomes]
rs1369324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289699	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28655102	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2870085	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825932	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4778716	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4778724	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4779112	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7496812	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][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	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
2	esv3428448	chr15:79236847-79239745	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1036938	CTSH	Cis_1M	lymphoblastoid	RTeQTL
rs1036938	CTSH	cis	Lymphoblastoid	GTEx
rs1036938	CTSH	cis	Muscle Skeletal	GTEx
rs1036938	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	chr15:79235400-79237600	Active TSS	Fetal Intestine Small	intestine
2	chr15:79235400-79237600	Active TSS	GM12878-XiMat	blood
3	chr15:79235400-79238000	Active TSS	Brain Hippocampus Middle	brain
4	chr15:79235600-79237600	Active TSS	Gastric	stomach
5	chr15:79236000-79237800	Active TSS	Fetal Intestine Large	intestine
6	chr15:79236000-79237800	Active TSS	Fetal Kidney	kidney
7	chr15:79236200-79237400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:79236200-79237400	Flanking Active TSS	Spleen	Spleen
9	chr15:79236200-79237800	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr15:79236200-79237800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:79236200-79237800	Active TSS	Psoas Muscle	Psoas
12	chr15:79236200-79237800	Flanking Active TSS	Right Ventricle	heart
13	chr15:79236200-79237800	Bivalent/Poised TSS	Thymus	Thymus
14	chr15:79236200-79238000	Active TSS	Brain Angular Gyrus	brain
15	chr15:79236400-79237400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
16	chr15:79236400-79237400	Flanking Active TSS	Esophagus	oesophagus
17	chr15:79236400-79237400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
18	chr15:79236400-79237400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
19	chr15:79236400-79237600	Flanking Active TSS	Pancreas	Pancrea
20	chr15:79236400-79237600	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr15:79236400-79237800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
22	chr15:79236400-79237800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:79236400-79237800	Active TSS	Brain Substantia Nigra	brain
24	chr15:79236400-79237800	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr15:79236400-79238000	Active TSS	H9 Cell Line	embryonic stem cell
26	chr15:79236400-79238000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:79236400-79238000	Bivalent Enhancer	Fetal Brain Male	brain
28	chr15:79236600-79237400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr15:79236600-79237400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:79236600-79237400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
31	chr15:79236600-79237400	Flanking Active TSS	HMEC	breast
32	chr15:79236600-79237800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
33	chr15:79236600-79237800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
34	chr15:79236600-79237800	Flanking Active TSS	Colonic Mucosa	Colon
35	chr15:79236600-79237800	Bivalent/Poised TSS	Fetal Lung	lung
36	chr15:79236600-79237800	Flanking Active TSS	Placenta	Placenta
37	chr15:79236600-79238000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr15:79236800-79237400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:79236800-79237400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:79236800-79237400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:79236800-79237400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:79236800-79237400	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr15:79236800-79237400	Active TSS	Small Intestine	intestine
44	chr15:79236800-79237400	Flanking Active TSS	Stomach Mucosa	stomach
45	chr15:79236800-79237400	Flanking Active TSS	Dnd41	blood
46	chr15:79236800-79237600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr15:79236800-79237800	Active TSS	Aorta	Aorta
48	chr15:79236800-79237800	Active TSS	Left Ventricle	heart
49	chr15:79236800-79238000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:79236800-79238000	Active TSS	Brain Cingulate Gyrus	brain

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