Variant report

Variant	rs1369324
Chromosome Location	chr15:79239719-79239720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:79238657..79240315-chr15:79242629..79245251,2	K562	blood:
2	chr15:79238426..79240913-chr15:79263614..79265466,3	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10152587	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10152589	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1036937	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1036938	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]
rs1036939	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10400877	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10400881	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10400902	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs11072815	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]
rs11072817	0.92[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11855406	0.92[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11856301	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12913968	0.90[EUR][1000 genomes]
rs2289699	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28655102	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2870085	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3825932	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4778716	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4778724	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4779112	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]
rs4779156	0.80[EUR][1000 genomes]
rs7496812	0.85[AMR][1000 genomes];0.96[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
rs1369324	CTSH	cis	Muscle Skeletal	GTEx
rs1369324	CTSH	cis	lymphoblastoid	seeQTL
rs1369324	CTSH	Cis_1M	lymphoblastoid	RTeQTL
rs1369324	CTSH	cis	multi-tissue	Pritchard

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79237800-79241000	Weak transcription	Liver	Liver
2	chr15:79237800-79241800	Weak transcription	Fetal Intestine Large	intestine
3	chr15:79237800-79242200	Weak transcription	Esophagus	oesophagus
4	chr15:79237800-79242200	Weak transcription	Fetal Kidney	kidney
5	chr15:79237800-79242400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:79237800-79242600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:79237800-79243600	Weak transcription	Right Atrium	heart
8	chr15:79237800-79243600	Weak transcription	Spleen	Spleen
9	chr15:79237800-79244200	Weak transcription	Psoas Muscle	Psoas
10	chr15:79238000-79242000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:79238000-79242000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr15:79238000-79242200	Weak transcription	Lung	lung
13	chr15:79238000-79242400	Weak transcription	Adipose Nuclei	Adipose
14	chr15:79238000-79243200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr15:79238000-79243400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:79238400-79241600	Weak transcription	Gastric	stomach
17	chr15:79238400-79241800	Weak transcription	Fetal Intestine Small	intestine
18	chr15:79238600-79241800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:79238600-79244200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:79238600-79252600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:79238800-79240800	Weak transcription	Stomach Mucosa	stomach
22	chr15:79238800-79241600	Weak transcription	Pancreas	Pancrea
23	chr15:79239000-79243600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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