Variant report

Variant	rs17641780
Chromosome Location	chr1:151659071-151659072
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151658558..151661445-chr1:151669676..151671900,2	K562	blood:
2	chr1:151657148..151660039-chr1:151734446..151736823,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143436	Chromatin interaction
ENSG00000143450	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1048694	0.92[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs10888428	0.84[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs11204866	0.90[EUR][1000 genomes]
rs11586679	0.88[EUR][1000 genomes]
rs1196352	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs1196357	0.92[CEU][hapmap];1.00[TSI][hapmap]
rs1196459	0.95[EUR][1000 genomes]
rs1196464	0.96[EUR][1000 genomes]
rs1196465	0.97[EUR][1000 genomes]
rs1201651	0.92[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1211981	0.92[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1308137	0.96[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1308139	0.95[EUR][1000 genomes]
rs1308143	0.97[EUR][1000 genomes]
rs1308145	0.92[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1308146	0.97[EUR][1000 genomes]
rs1308147	0.95[EUR][1000 genomes]
rs1308148	0.96[EUR][1000 genomes]
rs1308152	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs1308158	0.98[EUR][1000 genomes]
rs1607933	0.90[JPT][hapmap]
rs1717128	0.98[EUR][1000 genomes]
rs1781434	0.98[EUR][1000 genomes]
rs1891589	0.92[CEU][hapmap];1.00[TSI][hapmap]
rs2280475	0.85[JPT][hapmap]
rs2460996	0.93[EUR][1000 genomes]
rs2489892	0.97[EUR][1000 genomes]
rs2495392	0.92[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2495393	0.97[EUR][1000 genomes]
rs2495394	0.97[EUR][1000 genomes]
rs3204344	0.96[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34718348	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35981950	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3790512	0.84[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs4466658	0.90[JPT][hapmap]
rs6676545	0.90[JPT][hapmap]
rs6684548	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6685067	0.96[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6687866	0.96[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6690942	0.90[JPT][hapmap]
rs6702842	0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7534887	0.96[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17641780	SNX27	cis	Esophagus Mucosa	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151588200-151665200	Weak transcription	Aorta	Aorta
2	chr1:151591200-151675400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:151603000-151663200	Weak transcription	Colonic Mucosa	Colon
4	chr1:151610600-151665000	Weak transcription	Lung	lung
5	chr1:151611600-151668200	Weak transcription	Gastric	stomach
6	chr1:151618000-151667600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:151626800-151665400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:151627200-151659800	Weak transcription	Spleen	Spleen
9	chr1:151627200-151670600	Weak transcription	Small Intestine	intestine
10	chr1:151627400-151676000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:151628200-151669800	Weak transcription	Esophagus	oesophagus
12	chr1:151632200-151665000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:151632200-151667400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:151632400-151664400	Weak transcription	Thymus	Thymus
15	chr1:151638600-151675600	Weak transcription	Psoas Muscle	Psoas
16	chr1:151642000-151665000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:151642200-151659600	Weak transcription	HepG2	liver
18	chr1:151642200-151665000	Weak transcription	K562	blood
19	chr1:151642800-151665000	Weak transcription	Fetal Brain Female	brain
20	chr1:151643000-151665000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:151643600-151665000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:151643800-151669800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:151644000-151664600	Weak transcription	Fetal Thymus	thymus
24	chr1:151644000-151665000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:151644000-151665000	Weak transcription	Brain Angular Gyrus	brain
26	chr1:151644000-151665000	Weak transcription	Pancreas	Pancrea
27	chr1:151644200-151664400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:151644200-151665000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:151644200-151665000	Weak transcription	Ovary	ovary
30	chr1:151644200-151665200	Weak transcription	Brain Substantia Nigra	brain
31	chr1:151644400-151665000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:151644800-151665200	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:151646600-151665800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:151647800-151660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:151649000-151662000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:151650600-151663400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr1:151651200-151664800	Weak transcription	Brain Germinal Matrix	brain
38	chr1:151652800-151660000	Strong transcription	Fetal Intestine Large	intestine
39	chr1:151653000-151660000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:151653000-151661000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:151653200-151660000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:151653200-151660000	Strong transcription	Dnd41	blood
43	chr1:151653400-151665000	Weak transcription	HSMM	muscle
44	chr1:151653400-151669400	Weak transcription	HSMMtube	muscle
45	chr1:151653400-151671600	Weak transcription	Stomach Mucosa	stomach
46	chr1:151653600-151659200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:151653600-151659400	Weak transcription	GM12878-XiMat	blood
48	chr1:151653600-151662200	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr1:151653600-151665000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:151653600-151665000	Weak transcription	Osteobl	bone

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