Variant report

Variant	rs13062572
Chromosome Location	chr3:17120206-17120207
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	chr3:17118420..17120285-chr3:17121140..17122882,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11128818	0.84[EUR][1000 genomes]
rs11549706	0.93[CEU][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs13059760	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066204	1.00[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13073804	0.87[TSI][hapmap]
rs13073832	0.87[EUR][1000 genomes]
rs13077235	0.87[EUR][1000 genomes]
rs13085309	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];1.00[ASN][1000 genomes]
rs13089569	0.93[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs13097797	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17200543	0.87[TSI][hapmap]
rs17272754	0.84[TSI][hapmap]
rs17272810	1.00[ASW][hapmap];0.93[CEU][hapmap];0.84[TSI][hapmap];0.94[YRI][hapmap]
rs17272831	0.93[CEU][hapmap];0.84[TSI][hapmap]
rs34704046	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34937985	0.81[EUR][1000 genomes]
rs35185988	0.87[EUR][1000 genomes]
rs35281010	0.88[EUR][1000 genomes]
rs35545382	0.84[EUR][1000 genomes]
rs36118680	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935970	0.93[CEU][hapmap];0.84[TSI][hapmap]
rs62247257	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789069	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs7616589	0.93[CEU][hapmap]
rs7652293	0.93[CEU][hapmap];0.84[TSI][hapmap]
rs7652874	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9834723	0.92[CEU][hapmap]
rs9845137	0.93[CEU][hapmap]
rs9876768	0.93[CEU][hapmap];0.80[TSI][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13062572	COLQ	cis	parietal	SCAN
rs13062572	SATB1	cis	parietal	SCAN
rs13062572	SGOL1	cis	cerebellum	SCAN
rs13062572	TMEM43	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17089400-17135000	Weak transcription	Pancreas	Pancrea
2	chr3:17095400-17120600	Weak transcription	Aorta	Aorta
3	chr3:17095400-17120600	Weak transcription	Lung	lung
4	chr3:17097600-17120400	Weak transcription	Spleen	Spleen
5	chr3:17103400-17134400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr3:17107000-17133400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:17107200-17126200	Weak transcription	Fetal Kidney	kidney
8	chr3:17107600-17122800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:17108200-17120600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:17109800-17120800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:17110800-17132200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:17111400-17129400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:17111800-17130600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:17112000-17132000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr3:17112200-17137400	Weak transcription	Brain Germinal Matrix	brain
16	chr3:17112600-17120600	Weak transcription	Gastric	stomach
17	chr3:17112600-17120600	Weak transcription	Ovary	ovary
18	chr3:17112600-17120800	Weak transcription	Adipose Nuclei	Adipose
19	chr3:17112600-17123000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:17112600-17124000	Weak transcription	Fetal Intestine Large	intestine
21	chr3:17112600-17124600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:17112600-17126000	Weak transcription	Fetal Brain Female	brain
23	chr3:17112600-17127800	Weak transcription	Fetal Lung	lung
24	chr3:17112600-17129600	Weak transcription	Brain Angular Gyrus	brain
25	chr3:17112600-17130200	Weak transcription	Brain Anterior Caudate	brain
26	chr3:17112600-17135800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr3:17112800-17131200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:17112800-17135200	Weak transcription	Fetal Brain Male	brain
29	chr3:17114400-17126800	Strong transcription	Primary B cells from cord blood	blood
30	chr3:17114400-17131600	Weak transcription	Colonic Mucosa	Colon
31	chr3:17116000-17121200	Strong transcription	Placenta	Placenta
32	chr3:17116200-17120800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:17116400-17122200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:17116400-17122400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:17116400-17122800	Weak transcription	Fetal Thymus	thymus
36	chr3:17116600-17122800	Strong transcription	Primary T cells from cord blood	blood
37	chr3:17116800-17126000	Weak transcription	Dnd41	blood
38	chr3:17116800-17130200	Weak transcription	Thymus	Thymus
39	chr3:17117400-17125000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:17117400-17127600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:17117600-17120600	Weak transcription	Liver	Liver
42	chr3:17117800-17122600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:17117800-17127600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr3:17117800-17128000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr3:17118000-17121600	Strong transcription	Fetal Intestine Small	intestine
46	chr3:17118400-17120400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:17118400-17126800	Strong transcription	Primary B cells from peripheral blood	blood
48	chr3:17118600-17121000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr3:17118600-17126800	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr3:17119000-17122800	Strong transcription	Primary T helper cells fromperipheralblood	blood

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