Variant report

Variant	rs9863142
Chromosome Location	chr3:49366741-49366742
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49364331..49367707-chr3:49377216..49379882,3	MCF-7	breast:
2	chr3:49365884..49367486-chr3:49369396..49372019,2	K562	blood:

Variant related genes	Relation type
ENSG00000114316	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11707940	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11709788	0.95[ASN][1000 genomes]
rs11720964	0.83[ASN][1000 genomes]
rs11920251	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12497569	0.97[ASN][1000 genomes]
rs12715435	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13077498	0.85[CHD][hapmap]
rs13077723	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13078949	0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs1865741	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2230929	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2304442	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34142492	0.95[ASN][1000 genomes]
rs34366700	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34514189	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34566463	0.88[MKK][hapmap]
rs34567776	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34915642	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35446411	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35869135	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4410472	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4554002	0.90[ASN][1000 genomes]
rs4855842	0.85[CHB][hapmap]
rs4955431	0.97[ASN][1000 genomes]
rs56038006	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67882627	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6795772	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs73086105	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7640903	0.90[ASN][1000 genomes]
rs9814987	0.88[MKK][hapmap]
rs9818758	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9847839	0.88[MKK][hapmap]
rs9850917	1.00[JPT][hapmap]
rs9864406	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9873994	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9874474	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9883409	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs9863142	UQCRC1	cis	parietal	SCAN
rs9863142	CELSR3	cis	cerebellum	SCAN
rs9863142	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9863142	NICN1	cis	cerebellum	SCAN
rs9863142	NBEAL2	cis	cerebellum	SCAN
rs9863142	C3orf62	cis	cerebellum	SCAN
rs9863142	NDUFAF3	cis	parietal	SCAN
rs9863142	GPX1	cis	parietal	SCAN
rs9863142	USP4	cis	multi-tissue	Pritchard
rs9863142	RNF123	cis	parietal	SCAN
rs9863142	C3orf62	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49312600-49375800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:49315200-49373600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:49315200-49375000	Strong transcription	Fetal Stomach	stomach
4	chr3:49315400-49370400	Strong transcription	Fetal Thymus	thymus
5	chr3:49316200-49370200	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:49317200-49371800	Strong transcription	Fetal Intestine Small	intestine
7	chr3:49317400-49369400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:49317400-49370600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:49319200-49374800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:49319600-49371800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:49320200-49375000	Strong transcription	Thymus	Thymus
12	chr3:49320800-49368000	Strong transcription	Primary T cells from cord blood	blood
13	chr3:49321800-49373600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr3:49326800-49373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:49326800-49375000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:49333600-49369600	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr3:49335000-49369400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr3:49335000-49375000	Strong transcription	Placenta	Placenta
19	chr3:49335200-49369800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr3:49335200-49375200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr3:49338200-49375000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:49350400-49367600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:49350400-49370200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:49350400-49374800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:49350600-49369800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:49350600-49370600	Strong transcription	Adipose Nuclei	Adipose
27	chr3:49350800-49368000	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:49350800-49370400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:49351400-49367800	Strong transcription	Brain Hippocampus Middle	brain
30	chr3:49351400-49373000	Strong transcription	Duodenum Mucosa	Duodenum
31	chr3:49351400-49374200	Strong transcription	Dnd41	blood
32	chr3:49351600-49373400	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr3:49352000-49375000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:49352000-49375000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:49352200-49375000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:49352800-49374800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:49353000-49368000	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:49354200-49369600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:49354800-49366800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:49354800-49376600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr3:49355000-49370200	Strong transcription	Stomach Smooth Muscle	stomach
42	chr3:49355600-49367600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:49355600-49367800	Strong transcription	HUVEC	blood vessel
44	chr3:49357200-49367800	Strong transcription	Primary hematopoietic stem cells	blood
45	chr3:49357400-49367600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr3:49357400-49374800	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:49358000-49367600	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:49358000-49368000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:49360800-49367600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:49362600-49372000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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