Variant report

Variant	rs4779112
Chromosome Location	chr15:79220586-79220587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:79217212-79220767	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr15:79210927-79227564	K562	blood:	n/a	n/a
3	POLR2A	chr15:79220395-79220661	HepG2	liver:	n/a	n/a
4	POLR2A	chr15:79220572-79222607	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:79220287-79220616	HepG2	liver:	n/a	n/a
6	POLR2A	chr15:79217437-79220722	GM15510	blood:	n/a	n/a
7	POLR2A	chr15:79217371-79220785	K562	blood:	n/a	n/a
8	POLR2A	chr15:79220352-79220623	K562	blood:	n/a	n/a
9	POLR2A	chr15:79220329-79220669	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr15:79220251-79220670	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:79220111-79220613	HCT-116	colon:	n/a	n/a
12	POLR2A	chr15:79217306-79227452	GM12892	blood:	n/a	n/a
13	POLR2A	chr15:79218209-79220623	GM12878	blood:	n/a	n/a
14	POLR2A	chr15:79220200-79220756	H1-neurons	neurons:	n/a	n/a
15	POLR2A	chr15:79220277-79220746	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr15:79219148-79220767	K562	blood:	n/a	n/a
17	POLR2A	chr15:79217446-79220602	A549	lung:	n/a	n/a
18	POLR2A	chr15:79217342-79222654	GM12878	blood:	n/a	n/a
19	POLR2A	chr15:79211550-79222698	GM12878	blood:	n/a	n/a
20	POLR2A	chr15:79210815-79222697	GM12891	blood:	n/a	n/a
21	POLR2A	chr15:79220230-79220702	A549	lung:	n/a	n/a
22	POLR2A	chr15:79217356-79220698	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr15:79217378-79220689	GM19193	blood:	n/a	n/a
24	POLR2A	chr15:79219751-79220693	HUVEC	blood vessel:	n/a	n/a
25	FOSL2	chr15:79219213-79220695	HepG2	liver:	n/a	n/a
26	POLR2A	chr15:79220303-79220736	GM12891	blood:	n/a	n/a
27	POLR2A	chr15:79220179-79220786	U87	brain:	n/a	n/a
28	POLR2A	chr15:79219882-79220692	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr15:79219777-79220786	U87	brain:	n/a	n/a
30	POLR2A	chr15:79217326-79220672	GM18951	blood:	n/a	n/a
31	POLR2A	chr15:79220353-79220687	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr15:79218282-79220715	GM12892	blood:	n/a	n/a
33	POLR2A	chr15:79217480-79220739	GM19099	blood:	n/a	n/a
34	POLR2A	chr15:79220194-79220695	GM12878	blood:	n/a	n/a
35	POLR2A	chr15:79217632-79220622	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr15:79220185-79220711	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr15:79217474-79220810	GM12892	blood:	n/a	n/a
38	POLR2A	chr15:79220239-79220588	K562	blood:	n/a	n/a
39	POLR2A	chr15:79217215-79222665	PANC-1	pancreas:	n/a	n/a
40	POLR2A	chr15:79217202-79220812	GM12878	blood:	n/a	n/a
41	POLR2A	chr15:79217330-79220701	GM18526	blood:	n/a	n/a
42	POLR2A	chr15:79217321-79222679	GM18505	blood:	n/a	n/a
43	POLR2A	chr15:79218410-79220961	HepG2	liver:	n/a	n/a
44	POLR2A	chr15:79217362-79222442	K562	blood:	n/a	n/a
45	POLR2A	chr15:79220112-79220694	HL-60	blood:	n/a	n/a
46	POLR2A	chr15:79220206-79220691	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:79215592..79220788-chr15:79222055..79225592,6	MCF-7	breast:
2	chr15:79219384..79222077-chr15:79237429..79239448,2	MCF-7	breast:
3	chr15:79219205..79223895-chr15:79234790..79239038,6	MCF-7	breast:
4	chr15:79220482..79222111-chr15:79292818..79294616,2	MCF-7	breast:

No data

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

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10152587	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10152589	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1036937	1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1036938	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1036939	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10400877	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10400881	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10400902	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs11072815	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]
rs11072817	0.92[ASW][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072818	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11855406	0.92[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11856301	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1369324	0.84[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2289699	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28655102	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2870085	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3825932	0.83[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];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4778716	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4778724	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7496812	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4779112	CTSH	cis	lymphoblastoid	seeQTL
rs4779112	CTSH	Cis_1M	lymphoblastoid	RTeQTL
rs4779112	CTSH	cis	multi-tissue	Pritchard
rs4779112	CTSH	cis	Whole Blood	GTEx
rs4779112	CPLX3	cis	cerebellum	SCAN
rs4779112	CTSH	cis	Muscle Skeletal	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79190000-79222200	Strong transcription	Thymus	Thymus
2	chr15:79199800-79229400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:79203600-79231000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr15:79205400-79227800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:79205800-79223600	Weak transcription	Stomach Mucosa	stomach
6	chr15:79208200-79221800	Weak transcription	HMEC	breast
7	chr15:79208200-79223000	Weak transcription	Right Atrium	heart
8	chr15:79208400-79221000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:79208600-79223000	Weak transcription	Hela-S3	cervix
10	chr15:79209600-79220600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:79209800-79225800	Strong transcription	Fetal Stomach	stomach
12	chr15:79210000-79226600	Strong transcription	Duodenum Mucosa	Duodenum
13	chr15:79210000-79227200	Strong transcription	Primary B cells from peripheral blood	blood
14	chr15:79210200-79227000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:79210200-79228200	Strong transcription	GM12878-XiMat	blood
16	chr15:79210400-79220600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:79210400-79222200	Strong transcription	Liver	Liver
18	chr15:79210400-79226200	Strong transcription	Fetal Intestine Small	intestine
19	chr15:79210400-79228000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:79210400-79230200	Strong transcription	Fetal Intestine Large	intestine
21	chr15:79211600-79220600	Strong transcription	Primary T cells from cord blood	blood
22	chr15:79211600-79220600	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr15:79212000-79222400	Strong transcription	Left Ventricle	heart
24	chr15:79212200-79226000	Weak transcription	Fetal Brain Male	brain
25	chr15:79213400-79220600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:79213400-79220600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:79213400-79228400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:79213600-79220600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:79213600-79220600	Strong transcription	Aorta	Aorta
30	chr15:79213600-79220600	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr15:79213600-79220600	Strong transcription	Rectal Smooth Muscle	rectum
32	chr15:79213600-79220600	Strong transcription	Right Ventricle	heart
33	chr15:79213600-79220600	Strong transcription	HepG2	liver
34	chr15:79213600-79222200	Strong transcription	Pancreas	Pancrea
35	chr15:79214400-79221600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:79214600-79223000	Weak transcription	NHDF-Ad	bronchial
37	chr15:79214600-79229400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr15:79214800-79220800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:79214800-79221800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr15:79214800-79223200	Weak transcription	Psoas Muscle	Psoas
41	chr15:79215200-79221800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr15:79215200-79223000	Weak transcription	A549	lung
43	chr15:79215400-79220600	Strong transcription	Placenta	Placenta
44	chr15:79215400-79221200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:79215400-79222200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:79215400-79222200	Weak transcription	Osteobl	bone
47	chr15:79215400-79223400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr15:79215400-79233200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr15:79215400-79236600	Weak transcription	Small Intestine	intestine
50	chr15:79215600-79220600	Strong transcription	Brain Anterior Caudate	brain

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