Variant report

Variant	rs9876768
Chromosome Location	chr3:17049965-17049966
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	FAM48A	chr3:17049932-17050008	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PLCL2	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11549706	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs12054464	0.84[EUR][1000 genomes]
rs12233538	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs12233541	0.85[EUR][1000 genomes]
rs13059760	0.92[CEU][hapmap]
rs13062572	0.93[CEU][hapmap];0.80[TSI][hapmap]
rs13066204	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs13073804	0.82[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.92[TSI][hapmap]
rs13083189	0.84[EUR][1000 genomes]
rs13085309	0.93[CEU][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs13089569	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs13096536	0.94[EUR][1000 genomes]
rs17042926	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17200543	0.82[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.92[TSI][hapmap]
rs17272754	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.95[ASN][1000 genomes]
rs17272810	1.00[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs17272817	0.94[EUR][1000 genomes]
rs17272831	1.00[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs28498854	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34053933	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34126040	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34824028	0.95[EUR][1000 genomes]
rs35100600	0.90[EUR][1000 genomes]
rs35941157	0.93[ASN][1000 genomes]
rs3935970	1.00[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs4130495	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4290789	0.93[EUR][1000 genomes]
rs56060350	0.94[EUR][1000 genomes]
rs58855245	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59256854	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62247182	0.94[EUR][1000 genomes]
rs6442659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6769249	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6775782	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6778233	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6789069	0.93[CEU][hapmap];0.88[CHD][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs6805550	0.93[ASN][1000 genomes]
rs71627166	0.82[EUR][1000 genomes]
rs7616589	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7645276	0.93[ASN][1000 genomes]
rs7652293	1.00[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs7652874	0.93[CEU][hapmap]
rs9815788	0.82[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9834723	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9835432	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845137	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9845551	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9854926	1.00[YRI][hapmap]
rs9870977	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9881997	0.93[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9876768	COLQ	cis	cerebellum	SCAN
rs9876768	SATB1	cis	parietal	SCAN
rs9876768	COLQ	cis	parietal	SCAN
rs9876768	TMEM43	cis	cerebellum	SCAN
rs9876768	SGOL1	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17037000-17053200	Weak transcription	Fetal Intestine Small	intestine
2	chr3:17037600-17050800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr3:17040200-17051000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:17040200-17051200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr3:17041200-17051400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:17044000-17050800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:17045000-17053800	Weak transcription	Thymus	Thymus
8	chr3:17045200-17050000	Weak transcription	Lung	lung
9	chr3:17045200-17052200	Weak transcription	Aorta	Aorta
10	chr3:17045400-17051200	Weak transcription	Placenta	Placenta
11	chr3:17046200-17053200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:17046600-17050000	Enhancers	Primary T cells from cord blood	blood
13	chr3:17046600-17053000	Weak transcription	Brain Substantia Nigra	brain
14	chr3:17046800-17054200	Weak transcription	Psoas Muscle	Psoas
15	chr3:17046800-17054600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:17047000-17051800	Weak transcription	Fetal Brain Female	brain
17	chr3:17047000-17054200	Weak transcription	Brain Anterior Caudate	brain
18	chr3:17047800-17050000	Enhancers	GM12878-XiMat	blood
19	chr3:17048000-17050800	Weak transcription	Primary B cells from cord blood	blood
20	chr3:17048000-17051400	Weak transcription	Fetal Lung	lung
21	chr3:17048000-17051400	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:17048000-17051600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:17048000-17052600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:17048200-17051200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:17048200-17051200	Weak transcription	Fetal Thymus	thymus
26	chr3:17048200-17051200	Weak transcription	Left Ventricle	heart
27	chr3:17048200-17051200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:17048200-17051200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:17048200-17051200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:17048200-17051400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:17048200-17051400	Weak transcription	Adipose Nuclei	Adipose
32	chr3:17048200-17051600	Weak transcription	Fetal Kidney	kidney
33	chr3:17048200-17052000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:17048200-17052400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr3:17048200-17052600	Weak transcription	Spleen	Spleen
36	chr3:17048200-17053000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:17048200-17053000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:17048200-17053200	Weak transcription	Liver	Liver
39	chr3:17048200-17053200	Weak transcription	Stomach Mucosa	stomach
40	chr3:17048200-17054200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:17048200-17054600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:17048200-17054600	Weak transcription	Gastric	stomach
43	chr3:17048200-17054600	Weak transcription	Right Atrium	heart
44	chr3:17048200-17054800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:17048400-17051000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr3:17048400-17051200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:17048400-17051400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:17048400-17051400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:17048400-17051400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:17048400-17051800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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