Variant report

Variant	rs6505165
Chromosome Location	chr17:28574849-28574850
allele	C/T
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	chr17:28571737-28574999	K562	blood:	n/a	n/a
2	POLR2A	chr17:28574632-28574890	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:28574725..28577135-chr17:28599053..28600726,2	K562	blood:

Variant related genes	Relation type
ENSG00000252112	TF binding region
ENSG00000108578	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1050565	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs11867581	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12939390	0.94[JPT][hapmap]
rs12949747	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs13341611	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1487971	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]
rs17767256	0.94[JPT][hapmap]
rs2321705	0.82[ASN][1000 genomes]
rs3103305	0.82[ASN][1000 genomes]
rs3110452	0.94[JPT][hapmap]
rs3110453	0.82[ASN][1000 genomes]
rs33980254	0.94[JPT][hapmap]
rs3764449	0.94[JPT][hapmap]
rs3794806	0.94[JPT][hapmap]
rs3816828	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.82[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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6505169	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6505171	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6505173	0.85[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[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];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7208052	0.94[JPT][hapmap]
rs7210085	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7214014	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[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];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7214248	0.94[JPT][hapmap]
rs7214991	0.84[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7215330	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]
rs7223821	0.94[JPT][hapmap]
rs7342921	0.94[JPT][hapmap]
rs7342929	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8072345	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]
rs8073378	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8080300	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9896548	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6505165	GOSR1	cis	parietal	SCAN
rs6505165	SUZ12P	cis	parietal	SCAN
rs6505165	GIT1	cis	parietal	SCAN
rs6505165	SARM1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:28563200-28575000	Weak transcription	Aorta	Aorta
2	chr17:28565600-28575000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:28566000-28575400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr17:28566000-28575400	Weak transcription	Gastric	stomach
5	chr17:28566000-28575600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:28566600-28618000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:28567600-28598000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr17:28568800-28575000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr17:28569200-28575400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr17:28569400-28575000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr17:28569400-28575000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr17:28570000-28575200	Weak transcription	Fetal Lung	lung
13	chr17:28570200-28575000	Weak transcription	Left Ventricle	heart
14	chr17:28570200-28575200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr17:28570400-28576000	Weak transcription	Psoas Muscle	Psoas
16	chr17:28570400-28611600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr17:28570800-28596400	Weak transcription	Fetal Brain Male	brain
18	chr17:28571000-28575000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr17:28571000-28575000	Weak transcription	Brain Angular Gyrus	brain
20	chr17:28571000-28575000	Weak transcription	Pancreas	Pancrea
21	chr17:28571000-28575000	Weak transcription	Thymus	Thymus
22	chr17:28571000-28575200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:28571000-28575400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr17:28571000-28575600	Weak transcription	Right Atrium	heart
25	chr17:28571200-28575200	Weak transcription	Lung	lung
26	chr17:28571400-28575000	Weak transcription	Ovary	ovary
27	chr17:28571400-28575200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr17:28571400-28618000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr17:28571600-28575400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr17:28571600-28575400	Weak transcription	Fetal Heart	heart
31	chr17:28571600-28575600	Weak transcription	Colonic Mucosa	Colon
32	chr17:28571800-28575200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr17:28572000-28575000	Weak transcription	Esophagus	oesophagus
34	chr17:28572200-28575200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr17:28572200-28575400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr17:28572200-28607000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr17:28572400-28575400	Weak transcription	NH-A	brain
38	chr17:28572400-28583800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr17:28572400-28585600	Weak transcription	Right Ventricle	heart
40	chr17:28572400-28598000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr17:28572600-28575400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr17:28572600-28590600	Weak transcription	Stomach Mucosa	stomach
43	chr17:28572600-28598000	Weak transcription	Small Intestine	intestine
44	chr17:28572800-28580200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr17:28573000-28575000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr17:28573000-28575000	Weak transcription	Spleen	Spleen
47	chr17:28573000-28575600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr17:28573200-28577200	Strong transcription	Primary B cells from cord blood	blood
49	chr17:28573400-28575600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr17:28573400-28581000	Strong transcription	Primary T cells from cord blood	blood

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