Variant report

Variant	rs8072345
Chromosome Location	chr17:28604289-28604290
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	chr17:28603420..28605155-chr17:28616747..28619094,2	K562	blood:

Variant related genes	Relation type
ENSG00000108578	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1050565	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs11867581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12939390	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs12949747	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs13341611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1487971	0.84[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17767256	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs2321705	0.84[ASN][1000 genomes]
rs3103305	0.84[ASN][1000 genomes]
rs3110094	0.81[ASN][1000 genomes]
rs3110095	0.81[ASN][1000 genomes]
rs3110452	0.94[JPT][hapmap]
rs3110453	0.84[ASN][1000 genomes]
rs33980254	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs3764449	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs3794806	0.94[JPT][hapmap]
rs3816828	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505165	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6505169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6505171	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6505173	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7208052	0.94[JPT][hapmap]
rs7210085	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7214014	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7214248	0.94[JPT][hapmap]
rs7214991	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7215330	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7223821	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs7342921	0.94[JPT][hapmap]
rs7342929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8073378	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8080300	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9896548	0.86[EUR][1000 genomes];0.93[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	nsv1064975	chr17:28604187-28851905	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv543299	chr17:28604187-28851905	Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8072345	SUZ12P	cis	parietal	SCAN
rs8072345	GIT1	cis	parietal	SCAN
rs8072345	SARM1	cis	cerebellum	SCAN
rs8072345	GOSR1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:28566600-28618000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:28570400-28611600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:28571400-28618000	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr17:28572200-28607000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr17:28573800-28615400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr17:28574000-28616800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr17:28574600-28604600	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr17:28576200-28618000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr17:28579200-28616200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr17:28583000-28616600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr17:28583000-28616600	Strong transcription	Fetal Thymus	thymus
12	chr17:28583600-28604800	Strong transcription	Fetal Intestine Large	intestine
13	chr17:28583600-28616400	Strong transcription	Dnd41	blood
14	chr17:28583800-28604600	Strong transcription	K562	blood
15	chr17:28583800-28605000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr17:28586000-28617400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr17:28586600-28605000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr17:28588200-28615000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr17:28589200-28616400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr17:28589600-28616600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr17:28589800-28604600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr17:28590400-28612200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr17:28591200-28613400	Weak transcription	Pancreas	Pancrea
24	chr17:28591200-28617200	Weak transcription	Hela-S3	cervix
25	chr17:28591800-28616400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr17:28592400-28617200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr17:28592600-28615200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr17:28593400-28604800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr17:28596400-28605600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr17:28596600-28604400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr17:28596600-28604600	Strong transcription	Brain Cingulate Gyrus	brain
32	chr17:28596600-28616800	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr17:28598000-28616600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr17:28599600-28612000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr17:28599800-28616800	Strong transcription	A549	lung
36	chr17:28600000-28604800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr17:28600200-28612400	Weak transcription	Fetal Brain Male	brain
38	chr17:28600200-28613400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr17:28600400-28617200	Weak transcription	Psoas Muscle	Psoas
40	chr17:28600600-28618000	Weak transcription	Gastric	stomach
41	chr17:28600800-28605600	Weak transcription	Aorta	Aorta
42	chr17:28600800-28605600	Weak transcription	Spleen	Spleen
43	chr17:28600800-28611400	Weak transcription	Colon Smooth Muscle	Colon
44	chr17:28601000-28612400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr17:28601000-28617200	Weak transcription	Small Intestine	intestine
46	chr17:28601200-28605600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr17:28601200-28605600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr17:28601200-28605800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr17:28601200-28606600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr17:28601200-28608200	Weak transcription	Lung	lung

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