Variant report

Variant	rs11072815
Chromosome Location	chr15:79232319-79232320
allele	A/G
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	chr15:79230701-79233525	GM12891	blood:	n/a	n/a
2	RUNX3	chr15:79232117-79232605	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:79230656-79233528	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:79231539-79232524	GM12892	blood:	n/a	n/a
5	EBF1	chr15:79232166-79232458	GM12878	blood:	n/a	n/a
6	RELA	chr15:79230974-79232372	GM12891	blood:	n/a	chr15:79231380-79231389 chr15:79231380-79231389
7	MXI1	chr15:79232241-79232530	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:79232120-79232548	GM12878	blood:	n/a	n/a
9	ATF2	chr15:79232273-79232631	GM12878	blood:	n/a	n/a
10	CHD1	chr15:79230955-79232605	GM12878	blood:	n/a	n/a
11	MTA3	chr15:79230609-79232903	GM12878	blood:	n/a	n/a
12	BATF	chr15:79232241-79232453	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:79230799-79232596	GM12878	blood:	n/a	n/a
14	RUNX3	chr15:79232173-79232558	GM12878	blood:	n/a	n/a
15	EBF1	chr15:79232313-79232558	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:79231205-79232819	GM12878	blood:	n/a	n/a
17	FOXM1	chr15:79231019-79232411	GM12878	blood:	n/a	n/a
18	POLR2A	chr15:79230702-79232674	GM12878	blood:	n/a	n/a
19	POLR2A	chr15:79232068-79232501	GM12892	blood:	n/a	n/a
20	RELA	chr15:79230861-79232405	GM15510	blood:	n/a	chr15:79231380-79231389 chr15:79231380-79231389
21	WRNIP1	chr15:79232214-79232344	GM12878	blood:	n/a	n/a
22	MTA3	chr15:79232125-79232588	GM12878	blood:	n/a	n/a
23	PML	chr15:79230773-79232418	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:79229734..79233307-chr15:79235000..79238757,6	MCF-7	breast:
2	chr15:79222510..79224898-chr15:79231355..79233391,2	K562	blood:
3	chr15:79226655..79228594-chr15:79231638..79234454,2	MCF-7	breast:
4	chr15:79228950..79233188-chr15:79235013..79237607,6	K562	blood:
5	chr15:79228914..79232769-chr15:79235901..79239047,4	MCF-7	breast:

Variant related genes	Relation type
CTSH	TF binding region
ENSG00000103811	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10152587	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152589	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036937	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036938	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]
rs1036939	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10400877	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10400881	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10400902	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs11072817	0.85[ASW][hapmap];0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072818	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855406	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11856301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1369324	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289699	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28655102	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2870085	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825932	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4778716	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4778724	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4779112	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7496812	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11072815	CTSH	cis	multi-tissue	Pritchard
rs11072815	CTSH	cis	Lymphoblastoid	GTEx
rs11072815	CTSH	cis	lymphoblastoid	seeQTL
rs11072815	CTSH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79215400-79233200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr15:79215400-79236600	Weak transcription	Small Intestine	intestine
3	chr15:79215600-79232800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr15:79219600-79236200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:79220200-79235200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:79220600-79236200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:79220600-79236400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:79222200-79233400	Weak transcription	Thymus	Thymus
9	chr15:79222400-79236400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:79223800-79236000	Weak transcription	HSMMtube	muscle
11	chr15:79223800-79236200	Weak transcription	Brain Angular Gyrus	brain
12	chr15:79224200-79236400	Weak transcription	Colonic Mucosa	Colon
13	chr15:79224400-79236600	Weak transcription	HMEC	breast
14	chr15:79224600-79236200	Weak transcription	Psoas Muscle	Psoas
15	chr15:79225600-79236400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:79226400-79236000	Weak transcription	Fetal Kidney	kidney
17	chr15:79226600-79236200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr15:79227000-79236000	Weak transcription	Colon Smooth Muscle	Colon
19	chr15:79227200-79236000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:79227200-79236200	Weak transcription	Placenta	Placenta
21	chr15:79227400-79234800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr15:79227400-79236400	Weak transcription	Aorta	Aorta
23	chr15:79227400-79236600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:79227600-79236200	Weak transcription	Right Ventricle	heart
25	chr15:79228000-79236000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr15:79228200-79235400	Weak transcription	Brain Anterior Caudate	brain
27	chr15:79229000-79233200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr15:79229200-79232800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:79229400-79232400	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr15:79229800-79236200	Weak transcription	Esophagus	oesophagus
31	chr15:79230000-79235000	Weak transcription	Brain Hippocampus Middle	brain
32	chr15:79230000-79235600	Weak transcription	Fetal Stomach	stomach
33	chr15:79230000-79235600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:79230000-79235600	Weak transcription	Stomach Mucosa	stomach
35	chr15:79230000-79236200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr15:79230200-79232400	Enhancers	Adipose Nuclei	Adipose
37	chr15:79230200-79232600	Weak transcription	Gastric	stomach
38	chr15:79230200-79236000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr15:79230200-79236000	Weak transcription	Fetal Intestine Large	intestine
40	chr15:79230200-79236200	Weak transcription	Pancreas	Pancrea
41	chr15:79230200-79236200	Weak transcription	Spleen	Spleen
42	chr15:79230200-79236400	Weak transcription	Ovary	ovary
43	chr15:79230200-79236600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr15:79230400-79235200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr15:79230800-79232600	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr15:79231000-79236400	Weak transcription	Brain Substantia Nigra	brain
47	chr15:79231200-79235200	Weak transcription	Liver	Liver
48	chr15:79231400-79236000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:79231600-79232400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr15:79231800-79232400	Enhancers	Primary T cells fromperipheralblood	blood

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