Variant report

Variant	rs4682682
Chromosome Location	chr3:43387223-43387224
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10865932	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12634274	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs13065491	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13320571	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1384433	1.00[CHB][hapmap]
rs1395372	1.00[CHB][hapmap]
rs1588027	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs17075317	0.82[JPT][hapmap]
rs17075535	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17075558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17075596	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17075597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17075600	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17075630	0.82[CHB][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap]
rs17075705	1.00[CHB][hapmap]
rs17075743	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs17075792	1.00[CHB][hapmap]
rs2372372	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2372437	1.00[CHB][hapmap]
rs2888298	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4128529	1.00[CHB][hapmap]
rs4462942	1.00[CHB][hapmap]
rs4510359	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs4586783	1.00[CHB][hapmap]
rs4682678	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4682679	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4682685	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs4682882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683366	1.00[JPT][hapmap]
rs6441772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6441777	1.00[CHB][hapmap]
rs6770540	1.00[CHB][hapmap]
rs6783741	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs6791641	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799364	1.00[CHB][hapmap]
rs6800983	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs6803929	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621298	0.82[JPT][hapmap]
rs7623883	0.81[ASN][1000 genomes]
rs7628317	1.00[CHB][hapmap]
rs7649401	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9311339	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs9681394	0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs977911	1.00[CHB][hapmap];0.94[GIH][hapmap]
rs9834842	0.90[CEU][hapmap]
rs9836386	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9876172	0.88[MEX][hapmap];0.89[YRI][hapmap]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4682682	C1orf194	trans	brain	seeQTL
rs4682682	SLC47A2	trans	brain	seeQTL
rs4682682	FANK1	trans	brain	seeQTL
rs4682682	TEKT1	trans	brain	seeQTL
rs4682682	CAPSL	trans	brain	seeQTL
rs4682682	CAPS	trans	brain	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43373400-43393400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:43379600-43392800	Strong transcription	Placenta	Placenta
3	chr3:43380000-43387400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:43380000-43387600	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr3:43380000-43392200	Strong transcription	HepG2	liver
6	chr3:43380000-43392800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:43380800-43391800	Strong transcription	Fetal Stomach	stomach
8	chr3:43380800-43392600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:43380800-43392800	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr3:43380800-43392800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr3:43380800-43393000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:43380800-43393200	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:43381000-43388000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:43381000-43389400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr3:43381000-43392800	Weak transcription	Fetal Brain Male	brain
16	chr3:43381000-43393800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:43381000-43396400	Weak transcription	Stomach Mucosa	stomach
18	chr3:43381200-43388800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr3:43381200-43392800	Strong transcription	Fetal Intestine Large	intestine
20	chr3:43381400-43387600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:43381400-43392600	Strong transcription	Primary hematopoietic stem cells	blood
22	chr3:43381400-43392800	Strong transcription	Duodenum Mucosa	Duodenum
23	chr3:43381400-43393000	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:43381600-43387600	Strong transcription	NHEK	skin
25	chr3:43381600-43387800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:43381600-43392200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:43381800-43387600	Strong transcription	Aorta	Aorta
28	chr3:43381800-43392000	Strong transcription	Brain Anterior Caudate	brain
29	chr3:43381800-43392800	Strong transcription	Brain Germinal Matrix	brain
30	chr3:43382000-43387600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:43382000-43389200	Strong transcription	Fetal Kidney	kidney
32	chr3:43382000-43391600	Strong transcription	Fetal Intestine Small	intestine
33	chr3:43382000-43392200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:43382000-43392200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr3:43382000-43393400	Strong transcription	Primary B cells from cord blood	blood
36	chr3:43382200-43388400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:43382400-43388600	Weak transcription	A549	lung
38	chr3:43382400-43388800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:43382400-43388800	Weak transcription	K562	blood
40	chr3:43382400-43389000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:43382400-43391600	Genic enhancers	Primary T cells fromperipheralblood	blood
42	chr3:43382400-43392200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:43382400-43395400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:43382600-43388400	Weak transcription	Brain Substantia Nigra	brain
45	chr3:43382600-43392800	Strong transcription	Liver	Liver
46	chr3:43383000-43388800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr3:43383000-43391200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
48	chr3:43383200-43388800	Genic enhancers	Primary T cells from cord blood	blood
49	chr3:43383200-43391400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr3:43383200-43391600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood

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