Variant report

Variant	rs6797491
Chromosome Location	chr3:42608761-42608762
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	chr3:42607223..42608765-chr3:42608962..42611402,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1062051	0.81[TSI][hapmap]
rs13064597	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067987	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072295	0.82[EUR][1000 genomes]
rs13085143	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs13085695	0.82[EUR][1000 genomes]
rs13089845	0.82[EUR][1000 genomes]
rs13090902	0.82[EUR][1000 genomes]
rs13093680	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs13095447	0.82[EUR][1000 genomes]
rs13100261	1.00[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030458	0.97[EUR][1000 genomes]
rs17074662	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs17074673	0.82[EUR][1000 genomes]
rs17074674	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs17074693	0.82[EUR][1000 genomes]
rs2284303	0.82[EUR][1000 genomes]
rs2284304	0.82[EUR][1000 genomes]
rs2290976	0.90[CEU][hapmap];0.82[TSI][hapmap]
rs2300057	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs2300058	0.82[EUR][1000 genomes]
rs2302352	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs33969824	0.82[EUR][1000 genomes]
rs339705	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs339708	1.00[CEU][hapmap]
rs33984028	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs34077739	1.00[ASN][1000 genomes]
rs34196076	1.00[ASN][1000 genomes]
rs34243788	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683820	0.82[EUR][1000 genomes]
rs34687113	0.80[EUR][1000 genomes]
rs34762478	0.82[EUR][1000 genomes]
rs34801786	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs34852409	0.82[EUR][1000 genomes]
rs34977988	0.82[EUR][1000 genomes]
rs35216140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35384559	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35676838	0.82[EUR][1000 genomes]
rs35871059	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35890296	0.82[EUR][1000 genomes]
rs36033201	0.82[EUR][1000 genomes]
rs36043081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774401	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs3774402	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs3774404	0.82[EUR][1000 genomes]
rs3774407	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs3846058	0.82[EUR][1000 genomes]
rs3846059	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs3856737	0.82[EUR][1000 genomes]
rs3900780	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959327	1.00[ASN][1000 genomes]
rs55994846	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56047094	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56797870	0.82[EUR][1000 genomes]
rs57259216	0.82[EUR][1000 genomes]
rs58645732	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58825152	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58868911	0.82[EUR][1000 genomes]
rs59914338	0.82[EUR][1000 genomes]
rs60232916	0.82[EUR][1000 genomes]
rs60348477	0.82[EUR][1000 genomes]
rs60535002	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61149998	0.82[EUR][1000 genomes]
rs6441928	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs66786953	0.81[EUR][1000 genomes]
rs66933062	1.00[ASN][1000 genomes]
rs67059259	0.82[EUR][1000 genomes]
rs67174294	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67533173	0.80[EUR][1000 genomes]
rs67583158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771105	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778982	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6782164	0.82[EUR][1000 genomes]
rs67832425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788548	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs6790204	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]
rs6793186	0.82[EUR][1000 genomes]
rs6794643	1.00[ASN][1000 genomes]
rs6795296	0.82[EUR][1000 genomes]
rs6797545	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68004576	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68028490	0.82[EUR][1000 genomes]
rs68071013	0.82[EUR][1000 genomes]
rs71323162	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72864022	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72864072	0.82[EUR][1000 genomes]
rs73067957	1.00[ASN][1000 genomes]
rs73829255	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614219	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616701	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617403	0.82[EUR][1000 genomes]
rs7617736	0.82[EUR][1000 genomes]
rs7623867	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7624628	0.85[TSI][hapmap];0.82[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
rs6797491	C3orf39	cis	parietal	SCAN
rs6797491	NKTR	cis	cerebellum	SCAN
rs6797491	CCR1	cis	cerebellum	SCAN
rs6797491	SEC22C	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42587800-42611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:42588000-42613000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:42588400-42613000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:42588600-42618000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:42589000-42611800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:42589200-42611000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:42589400-42610800	Weak transcription	Stomach Mucosa	stomach
8	chr3:42589400-42611000	Strong transcription	Fetal Stomach	stomach
9	chr3:42589400-42612400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:42589400-42614000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:42589600-42611200	Strong transcription	Fetal Intestine Small	intestine
12	chr3:42589600-42611800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:42589800-42610600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:42589800-42611000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:42589800-42616400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:42590000-42611600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr3:42590000-42612600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr3:42590200-42611600	Strong transcription	Fetal Muscle Leg	muscle
19	chr3:42590200-42611800	Strong transcription	Adipose Nuclei	Adipose
20	chr3:42591000-42609200	Strong transcription	Fetal Intestine Large	intestine
21	chr3:42591000-42614000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:42591200-42610400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:42591200-42611800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:42591400-42611200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:42591600-42609400	Strong transcription	Primary B cells from cord blood	blood
26	chr3:42591600-42611800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:42591800-42609400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:42591800-42609400	Strong transcription	Fetal Lung	lung
29	chr3:42591800-42610600	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:42592000-42611800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:42592800-42609200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:42592800-42609200	Strong transcription	Placenta	Placenta
33	chr3:42592800-42610600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:42593400-42611000	Strong transcription	Liver	Liver
35	chr3:42593400-42612000	Strong transcription	Primary B cells from peripheral blood	blood
36	chr3:42593600-42611600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:42593800-42611600	Strong transcription	Fetal Brain Female	brain
38	chr3:42594400-42611600	Strong transcription	Stomach Smooth Muscle	stomach
39	chr3:42594600-42615200	Strong transcription	Fetal Muscle Trunk	muscle
40	chr3:42594800-42610800	Weak transcription	Fetal Heart	heart
41	chr3:42597600-42609000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr3:42598000-42611400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:42598000-42615600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:42598200-42611000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:42598200-42616400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:42598400-42609000	Strong transcription	GM12878-XiMat	blood
47	chr3:42598400-42611800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:42598600-42611600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:42598600-42612800	Strong transcription	Fetal Thymus	thymus
50	chr3:42599600-42612200	Strong transcription	Dnd41	blood

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