Variant report

Variant	rs17549345
Chromosome Location	chr3:88080579-88080580
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:88079170..88082380-chr3:88083202..88085793,3	MCF-7	breast:
2	chr3:88080562..88082885-chr3:88098755..88100923,2	MCF-7	breast:
3	chr3:88079258..88082127-chr3:88106343..88109218,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229729	Chromatin interaction
ENSG00000163320	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10511136	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11128018	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11128019	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717413	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11915058	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714696	1.00[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs13074576	0.84[EUR][1000 genomes]
rs1431153	0.87[EUR][1000 genomes]
rs1469569	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1503433	1.00[CEU][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs1604699	0.84[EUR][1000 genomes]
rs17549213	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1835542	0.87[EUR][1000 genomes]
rs1835543	0.83[EUR][1000 genomes]
rs2016224	1.00[CEU][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs2099229	0.84[EUR][1000 genomes]
rs2163423	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2344185	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2880801	0.84[EUR][1000 genomes]
rs2880802	0.84[EUR][1000 genomes]
rs35040143	0.87[EUR][1000 genomes]
rs4858925	0.84[EUR][1000 genomes]
rs4858969	0.84[EUR][1000 genomes]
rs4858971	0.83[EUR][1000 genomes]
rs4858972	0.83[EUR][1000 genomes]
rs4858974	0.87[EUR][1000 genomes]
rs4858975	0.87[EUR][1000 genomes]
rs55644022	0.81[ASN][1000 genomes]
rs55840331	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006017	0.86[ASN][1000 genomes]
rs56173847	0.88[ASN][1000 genomes]
rs60099577	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551264	0.81[ASN][1000 genomes]
rs67047416	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770013	0.83[EUR][1000 genomes]
rs6778211	0.84[EUR][1000 genomes]
rs6781226	0.84[EUR][1000 genomes]
rs6781901	0.87[EUR][1000 genomes]
rs6785333	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68042814	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73144053	0.82[ASN][1000 genomes]
rs7629565	0.84[EUR][1000 genomes]
rs7630716	1.00[CEU][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs7637503	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7652406	0.84[EUR][1000 genomes]
rs9310061	0.87[EUR][1000 genomes]
rs9852704	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9855839	0.84[EUR][1000 genomes]
rs9859034	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9861809	0.84[EUR][1000 genomes]
rs9863076	1.00[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs9878862	0.84[EUR][1000 genomes]
rs9880480	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877146	chr3:87983962-88159835	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv536635	chr3:88049304-88088520	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17549345	HTR1F	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88073600-88080600	Weak transcription	Thymus	Thymus
2	chr3:88078200-88080800	Weak transcription	Left Ventricle	heart
3	chr3:88079200-88080600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:88079200-88081400	Active TSS	GM12878-XiMat	blood
5	chr3:88079400-88081800	Active TSS	NHDF-Ad	bronchial
6	chr3:88079600-88080600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr3:88079600-88080600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:88079600-88080600	Enhancers	Stomach Mucosa	stomach
9	chr3:88079600-88080800	Enhancers	HepG2	liver
10	chr3:88079800-88080600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr3:88079800-88080600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:88079800-88080600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr3:88079800-88080600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:88079800-88080600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:88079800-88080600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:88079800-88080600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:88079800-88080600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:88079800-88080600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:88079800-88080600	Enhancers	HUVEC	blood vessel
20	chr3:88079800-88080600	Weak transcription	NHLF	lung
21	chr3:88079800-88080600	Enhancers	Osteobl	bone
22	chr3:88079800-88080800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr3:88079800-88080800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:88079800-88080800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:88079800-88080800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:88080000-88080600	Enhancers	Liver	Liver
27	chr3:88080000-88081200	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr3:88080000-88084400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:88080200-88080600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:88080200-88080600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr3:88080200-88080600	Enhancers	A549	lung
32	chr3:88080400-88080600	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr3:88080400-88080600	Enhancers	Primary B cells from cord blood	blood
34	chr3:88080400-88080600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:88080400-88080600	Enhancers	Adipose Nuclei	Adipose
36	chr3:88080400-88080600	Enhancers	Colon Smooth Muscle	Colon
37	chr3:88080400-88080600	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr3:88080400-88080600	Enhancers	Rectal Smooth Muscle	rectum
39	chr3:88080400-88080600	Enhancers	NH-A	brain
40	chr3:88080400-88080800	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr3:88080400-88080800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:88080400-88080800	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr3:88080400-88080800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr3:88080400-88080800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr3:88080400-88080800	Enhancers	Hela-S3	cervix
46	chr3:88080400-88081000	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr3:88080400-88081000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:88080400-88081000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr3:88080400-88081000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr3:88080400-88081200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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