Variant report

Variant	rs12949747
Chromosome Location	chr17:28584358-28584359
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1050565	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];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11656408	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11867581	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs11870192	0.87[AMR][1000 genomes]
rs12938714	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12939390	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12941223	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12945042	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12947654	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13341611	0.93[JPT][hapmap]
rs1487971	0.84[CEU][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs17767256	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2321706	0.80[ASN][1000 genomes]
rs3103303	0.82[ASN][1000 genomes]
rs3103306	0.80[ASN][1000 genomes]
rs3110452	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs33980254	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][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]
rs34353378	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34622227	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35724800	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36000555	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36048853	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3764449	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3794806	1.00[CEU][hapmap];0.86[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];0.93[ASN][1000 genomes]
rs3816828	0.94[JPT][hapmap]
rs6505165	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs6505169	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs6505173	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs7208052	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7210085	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs7214014	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs7214248	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7214991	0.84[CEU][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs7215330	0.84[CEU][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs7223821	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73268099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7342921	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7342929	0.94[JPT][hapmap]
rs8072345	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs8078900	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8080149	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12949747	BLMH	Cis_1M	lymphoblastoid	RTeQTL
rs12949747	CPD	cis	parietal	SCAN
rs12949747	GOSR1	cis	parietal	SCAN

Chromatin state (count:124 , 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	chr17:28567600-28598000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr17:28570400-28611600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr17:28570800-28596400	Weak transcription	Fetal Brain Male	brain
5	chr17:28571400-28618000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr17:28572200-28607000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr17:28572400-28585600	Weak transcription	Right Ventricle	heart
8	chr17:28572400-28598000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr17:28572600-28590600	Weak transcription	Stomach Mucosa	stomach
10	chr17:28572600-28598000	Weak transcription	Small Intestine	intestine
11	chr17:28573600-28588800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr17:28573600-28590800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr17:28573800-28595600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr17:28573800-28615400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr17:28574000-28595200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr17:28574000-28616800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr17:28574400-28591000	Weak transcription	Hela-S3	cervix
18	chr17:28574600-28604600	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr17:28576000-28594600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr17:28576200-28591000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr17:28576200-28592200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr17:28576200-28599200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr17:28576200-28599400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr17:28576200-28618000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr17:28576400-28584600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr17:28576600-28586200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr17:28576600-28590600	Weak transcription	Psoas Muscle	Psoas
28	chr17:28576800-28584600	Weak transcription	Brain Germinal Matrix	brain
29	chr17:28576800-28585600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr17:28576800-28590600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr17:28577000-28586400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr17:28577000-28588600	Weak transcription	Brain Angular Gyrus	brain
33	chr17:28577000-28589600	Weak transcription	Pancreas	Pancrea
34	chr17:28577000-28593600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr17:28577000-28597800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr17:28577000-28598200	Weak transcription	Colonic Mucosa	Colon
37	chr17:28578200-28586800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr17:28578400-28594000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr17:28578600-28586000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr17:28579200-28616200	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr17:28580600-28584800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr17:28580600-28584800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr17:28580600-28585600	Weak transcription	Gastric	stomach
44	chr17:28580600-28586000	Weak transcription	Lung	lung
45	chr17:28580600-28586800	Weak transcription	NH-A	brain
46	chr17:28580600-28599200	Weak transcription	NHLF	lung
47	chr17:28580800-28584800	Weak transcription	Ovary	ovary
48	chr17:28580800-28585000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr17:28580800-28585600	Weak transcription	Aorta	Aorta
50	chr17:28580800-28585600	Weak transcription	Esophagus	oesophagus

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