Variant report

Variant	rs1827158
Chromosome Location	chr3:98621665-98621666
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr3:98620719-98621687	A549	lung:	n/a	n/a
2	MAZ	chr3:98619241-98621681	IMR90	lung:	n/a	n/a
3	GATA3	chr3:98621173-98621780	SH-SY5Y	brain:	n/a	n/a
4	GATA2	chr3:98619874-98621719	SH-SY5Y	brain:	n/a	chr3:98621157-98621168
5	GATA3	chr3:98619677-98621668	A549	lung:	n/a	chr3:98621157-98621168
6	TCF7L2	chr3:98621397-98621772	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:98618257-98622361	U87	brain:	n/a	n/a
8	POLR2A	chr3:98619206-98621801	HCT-116	colon:	n/a	n/a
9	POLR2A	chr3:98618299-98622361	U87	brain:	n/a	n/a
10	GTF2F1	chr3:98621640-98621674	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:98618148-98622423	U87	brain:	n/a	n/a
12	POLR2A	chr3:98620645-98621727	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr3:98621425-98621688	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr3:98618120-98622417	U87	brain:	n/a	n/a
15	CHD1	chr3:98618292-98622396	IMR90	lung:	n/a	chr3:98620361-98620371
16	MXI1	chr3:98618881-98621804	IMR90	lung:	n/a	n/a
17	TCF12	chr3:98618229-98622320	A549	lung:	n/a	n/a
18	POLR2A	chr3:98615281-98622405	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98620298..98622928-chr3:98626076..98627807,2	MCF-7	breast:

Variant related genes	Relation type
DCBLD2	TF binding region
ENSG00000207331	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10433438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511169	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511171	0.84[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10935518	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935542	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935564	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11708475	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716000	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716007	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716281	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716579	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719660	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914591	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11916285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11918243	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11918944	0.91[ASN][1000 genomes]
rs11920205	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11920327	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11922078	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11923486	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11923805	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11928233	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13069458	0.91[ASN][1000 genomes]
rs1440154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1471588	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16840260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17210963	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs17212369	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17213336	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17278047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17278278	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17852693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1822017	0.94[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2278599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3772100	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55650073	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55662129	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55730510	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55764252	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55988144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075614	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56290036	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56322058	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276861	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276862	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62276864	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276869	0.91[ASN][1000 genomes]
rs62276879	0.85[ASN][1000 genomes]
rs62276883	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276884	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276885	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276888	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276909	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6440253	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66517942	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6805605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136038	0.89[EUR][1000 genomes]
rs73136045	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73136048	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73136057	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73136060	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73138004	0.91[EUR][1000 genomes]
rs73138027	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138030	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138048	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138053	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138055	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138058	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73138063	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138082	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140027	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73140032	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7432439	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7614892	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629550	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638009	0.91[ASN][1000 genomes]
rs7642785	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644946	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8179927	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs982291	0.91[ASN][1000 genomes]

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	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1827158	OR5K2	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98617400-98622000	Active TSS	Right Ventricle	heart
2	chr3:98618200-98621800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:98618400-98621800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:98618600-98621800	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr3:98618600-98621800	Active TSS	HSMMtube	muscle
6	chr3:98618800-98621800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr3:98618800-98622200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:98619800-98621800	Active TSS	Fetal Brain Female	brain
9	chr3:98621000-98621800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:98621000-98621800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr3:98621000-98621800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:98621000-98621800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:98621000-98622000	Flanking Active TSS	NH-A	brain
14	chr3:98621000-98622200	Flanking Active TSS	NHEK	skin
15	chr3:98621200-98621800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:98621200-98621800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr3:98621200-98621800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr3:98621200-98621800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr3:98621200-98621800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:98621200-98621800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:98621200-98621800	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr3:98621200-98621800	Flanking Active TSS	Fetal Heart	heart
23	chr3:98621200-98621800	Flanking Active TSS	Fetal Kidney	kidney
24	chr3:98621200-98621800	Flanking Active TSS	Rectal Smooth Muscle	rectum
25	chr3:98621200-98621800	Flanking Active TSS	Dnd41	blood
26	chr3:98621200-98621800	Flanking Active TSS	NHDF-Ad	bronchial
27	chr3:98621200-98621800	Flanking Active TSS	NHLF	lung
28	chr3:98621200-98622000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr3:98621200-98622000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:98621200-98622200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:98621200-98622400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:98621200-98622400	Flanking Active TSS	A549	lung
33	chr3:98621200-98622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:98621400-98621800	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr3:98621400-98621800	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr3:98621400-98621800	Enhancers	Liver	Liver
37	chr3:98621400-98621800	Flanking Active TSS	Brain Angular Gyrus	brain
38	chr3:98621400-98621800	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr3:98621400-98621800	Enhancers	HUVEC	blood vessel
40	chr3:98621400-98622000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:98621400-98622000	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr3:98621400-98622200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:98621400-98622200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:98621400-98622200	Enhancers	HSMM	muscle
45	chr3:98621400-98622600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr3:98621400-98625000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:98621600-98621800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:98621600-98621800	Enhancers	Primary T cells from cord blood	blood
49	chr3:98621600-98621800	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr3:98621600-98621800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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