Variant report

Variant	rs1040501
Chromosome Location	chr1:169088314-169088315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169087143..169088781-chr1:169092217..169094524,2	K562	blood:
2	chr1:169087281..169089561-chr1:169092217..169094257,2	K562	blood:
3	chr1:169087780..169089721-chr1:169091214..169093379,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1040500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1080268	1.00[CEU][hapmap]
rs10919064	0.89[CHB][hapmap]
rs11809180	0.82[MEX][hapmap]
rs1200150	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs1208373	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12084964	0.82[MEX][hapmap]
rs12748624	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12751379	1.00[CEU][hapmap]
rs1320964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1320966	1.00[CEU][hapmap]
rs16828165	1.00[CEU][hapmap]
rs16861997	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];1.00[EUR][1000 genomes]
rs16862051	1.00[CEU][hapmap]
rs16862081	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2066001	1.00[CEU][hapmap];0.92[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs35207260	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35471075	1.00[EUR][1000 genomes]
rs35527028	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36040633	1.00[CEU][hapmap]
rs3753292	0.90[CHB][hapmap]
rs3753299	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3766033	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766034	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766038	0.90[CHB][hapmap]
rs3766039	0.90[CHB][hapmap]
rs3766048	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3766049	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3766072	1.00[EUR][1000 genomes]
rs3766075	1.00[CEU][hapmap]
rs3766083	1.00[CEU][hapmap]
rs3766084	1.00[CEU][hapmap]
rs3820054	0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41442344	1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs6675220	1.00[CEU][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap]
rs7528751	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1040501	FFAR1	trans	lymphoblastoid	seeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169079800-169094600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr1:169079800-169105800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:169080200-169088800	Genic enhancers	Hela-S3	cervix
4	chr1:169080200-169089800	Genic enhancers	Fetal Intestine Large	intestine
5	chr1:169081000-169098200	Weak transcription	Small Intestine	intestine
6	chr1:169081200-169091800	Strong transcription	Fetal Brain Female	brain
7	chr1:169082200-169097600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:169082400-169097400	Weak transcription	Fetal Thymus	thymus
9	chr1:169083400-169088600	Weak transcription	HSMMtube	muscle
10	chr1:169083400-169090400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:169083600-169094600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:169084000-169088400	Weak transcription	NHDF-Ad	bronchial
13	chr1:169084000-169088800	Weak transcription	Ovary	ovary
14	chr1:169084000-169094000	Weak transcription	Primary T cells from cord blood	blood
15	chr1:169084200-169099200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:169084800-169089600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:169085000-169089600	Transcr. at gene 5' and 3'	A549	lung
18	chr1:169085200-169088400	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:169085400-169090800	Enhancers	NHLF	lung
20	chr1:169085400-169091000	Genic enhancers	HepG2	liver
21	chr1:169085400-169097600	Weak transcription	Fetal Brain Male	brain
22	chr1:169085400-169102200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:169085600-169088400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:169085600-169088400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:169085600-169088800	Weak transcription	K562	blood
26	chr1:169085600-169089200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:169085600-169090400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:169085600-169090800	Weak transcription	Lung	lung
29	chr1:169085600-169091000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:169085600-169091200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:169085600-169091800	Genic enhancers	Rectal Mucosa Donor 31	rectum
32	chr1:169085600-169092400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:169085600-169094800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr1:169085600-169096600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:169085800-169088400	Genic enhancers	Brain Inferior Temporal Lobe	brain
36	chr1:169085800-169088600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:169085800-169088600	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:169085800-169089200	Genic enhancers	Brain Anterior Caudate	brain
39	chr1:169085800-169089600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:169085800-169089600	Enhancers	NHEK	skin
41	chr1:169085800-169090800	Weak transcription	Aorta	Aorta
42	chr1:169085800-169090800	Weak transcription	Spleen	Spleen
43	chr1:169085800-169091000	Weak transcription	Right Atrium	heart
44	chr1:169085800-169091400	Genic enhancers	Duodenum Mucosa	Duodenum
45	chr1:169085800-169094000	Weak transcription	Placenta	Placenta
46	chr1:169085800-169097400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:169085800-169100000	Weak transcription	Thymus	Thymus
48	chr1:169086000-169088600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:169086000-169088600	Weak transcription	Fetal Stomach	stomach
50	chr1:169086200-169094200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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