Variant report

Variant	rs6790204
Chromosome Location	chr3:42677914-42677915
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	chr3:42677644..42680168-chr3:42693244..42695506,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114853	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs13064597	0.81[EUR][1000 genomes]
rs13067987	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13072295	0.81[EUR][1000 genomes]
rs13085143	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs13085695	0.81[EUR][1000 genomes]
rs13089845	0.81[EUR][1000 genomes]
rs13090902	0.81[EUR][1000 genomes]
rs13093680	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs13095447	0.81[EUR][1000 genomes]
rs13100261	1.00[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs17030458	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17074662	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs17074673	0.81[EUR][1000 genomes]
rs17074674	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs17074693	0.81[EUR][1000 genomes]
rs2284303	0.81[EUR][1000 genomes]
rs2284304	0.81[EUR][1000 genomes]
rs2290976	0.90[CEU][hapmap]
rs2300057	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs2300058	0.81[EUR][1000 genomes]
rs2302352	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs33969824	0.81[EUR][1000 genomes]
rs339705	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs339708	1.00[CEU][hapmap]
rs33984028	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs34077739	0.80[EUR][1000 genomes]
rs34196076	0.80[EUR][1000 genomes]
rs34243788	0.83[EUR][1000 genomes]
rs34683820	0.81[EUR][1000 genomes]
rs34762478	0.81[EUR][1000 genomes]
rs34801786	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs34852409	0.81[EUR][1000 genomes]
rs34977988	0.81[EUR][1000 genomes]
rs35216140	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35384559	0.83[EUR][1000 genomes]
rs35676838	0.81[EUR][1000 genomes]
rs35871059	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35890296	0.81[EUR][1000 genomes]
rs36033201	0.81[EUR][1000 genomes]
rs36043081	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3774401	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs3774402	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs3774404	0.81[EUR][1000 genomes]
rs3774407	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs3846058	0.81[EUR][1000 genomes]
rs3846059	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs3856737	0.81[EUR][1000 genomes]
rs3900780	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55994846	0.94[EUR][1000 genomes]
rs56047094	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56797870	0.81[EUR][1000 genomes]
rs57259216	0.81[EUR][1000 genomes]
rs58645732	0.83[EUR][1000 genomes]
rs58825152	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58868911	0.81[EUR][1000 genomes]
rs59914338	0.81[EUR][1000 genomes]
rs60232916	0.81[EUR][1000 genomes]
rs60348477	0.81[EUR][1000 genomes]
rs60535002	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61149998	0.81[EUR][1000 genomes]
rs6441928	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs67059259	0.81[EUR][1000 genomes]
rs67174294	0.81[EUR][1000 genomes]
rs67583158	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6771105	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6778982	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6782164	0.81[EUR][1000 genomes]
rs67832425	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6788548	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs6793186	0.81[EUR][1000 genomes]
rs6795296	0.81[EUR][1000 genomes]
rs6797491	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6797545	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs68004576	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs68028490	0.81[EUR][1000 genomes]
rs68071013	0.81[EUR][1000 genomes]
rs71323162	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72864022	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72864072	0.81[EUR][1000 genomes]
rs73829255	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7614219	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7616701	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7617403	0.81[EUR][1000 genomes]
rs7617736	0.81[EUR][1000 genomes]
rs7623867	0.97[EUR][1000 genomes]
rs7624628	0.81[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6790204	C3orf39	cis	parietal	SCAN
rs6790204	CCR1	cis	cerebellum	SCAN
rs6790204	SEC22C	cis	Muscle Skeletal	GTEx
rs6790204	NKTR	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42647200-42688200	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr3:42651200-42693000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:42651800-42680400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:42656200-42688400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:42657400-42679600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:42658200-42682200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:42658200-42693000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:42658400-42691400	Strong transcription	Dnd41	blood
9	chr3:42658600-42678400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:42659000-42688000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:42660000-42679000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:42665000-42679400	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr3:42668000-42688200	Strong transcription	Fetal Thymus	thymus
14	chr3:42668400-42692800	Strong transcription	Fetal Muscle Trunk	muscle
15	chr3:42668600-42678200	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr3:42668800-42679800	Strong transcription	Osteobl	bone
17	chr3:42668800-42689200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:42668800-42690200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:42669000-42690600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:42669200-42691800	Strong transcription	Fetal Intestine Large	intestine
21	chr3:42669200-42692200	Strong transcription	Liver	Liver
22	chr3:42669400-42690600	Strong transcription	K562	blood
23	chr3:42669400-42691600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:42669400-42692200	Strong transcription	Fetal Muscle Leg	muscle
25	chr3:42669600-42690000	Strong transcription	Primary B cells from peripheral blood	blood
26	chr3:42669600-42691000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:42669800-42679600	Strong transcription	Duodenum Mucosa	Duodenum
28	chr3:42669800-42680600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:42670200-42678400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:42671000-42690800	Strong transcription	Placenta	Placenta
31	chr3:42671200-42678800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:42671200-42679000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:42671200-42681400	Strong transcription	Fetal Brain Male	brain
34	chr3:42671200-42690800	Strong transcription	NHDF-Ad	bronchial
35	chr3:42671200-42691400	Strong transcription	HSMM	muscle
36	chr3:42671200-42691600	Strong transcription	NH-A	brain
37	chr3:42671400-42678200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:42671400-42680400	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:42671400-42680600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:42671400-42682000	Strong transcription	NHEK	skin
41	chr3:42671400-42682200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:42671400-42682200	Strong transcription	HUVEC	blood vessel
43	chr3:42671400-42683000	Strong transcription	HSMMtube	muscle
44	chr3:42671400-42687600	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:42671400-42689800	Strong transcription	Primary B cells from cord blood	blood
46	chr3:42671400-42690600	Strong transcription	Fetal Lung	lung
47	chr3:42671400-42692200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:42671400-42692200	Strong transcription	Adipose Nuclei	Adipose
49	chr3:42671800-42679000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:42671800-42683000	Strong transcription	Sigmoid Colon	Sigmoid Colon

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