Variant report

Variant	rs273250
Chromosome Location	chr1:79115306-79115307
allele	A/G
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	POLR2A	chr1:79115298-79115703	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr1:79107167-79118433	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:79115219-79115798	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:79115299-79117884	GM19099	blood:	n/a	n/a
5	POLR2A	chr1:79115240-79115772	SK-N-MC	brain:	n/a	n/a
6	TBP	chr1:79115302-79116263	GM12878	blood:	n/a	n/a
7	NFIC	chr1:79115085-79115848	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr1:79115254-79115876	U87	brain:	n/a	n/a
9	POLR2A	chr1:79115218-79115979	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr1:79115245-79115707	MCF10A-Er-Src	breast:	n/a	n/a
11	PML	chr1:79115235-79115727	GM12878	blood:	n/a	n/a
12	ELK1	chr1:79115218-79115700	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:79115290-79116266	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:79115220-79115859	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr1:79115254-79115870	U87	brain:	n/a	n/a
16	NFIC	chr1:79115132-79115712	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr1:79115261-79115648	GM12892	blood:	n/a	n/a
18	POLR2A	chr1:79115249-79116235	GM18505	blood:	n/a	n/a
19	POLR2A	chr1:79114913-79118476	GM18951	blood:	n/a	n/a
20	PAX5	chr1:79115297-79115655	GM12878	blood:	n/a	chr1:79115456-79115465
21	POLR2A	chr1:79115264-79115682	GM12892	blood:	n/a	n/a
22	POLR2A	chr1:79115182-79115738	GM19193	blood:	n/a	n/a
23	POLR2A	chr1:79115289-79115692	HUVEC	blood vessel:	n/a	n/a
24	MXI1	chr1:79115150-79115678	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
IFI44	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1107320	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109244	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11162523	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162536	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11162537	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11162539	0.81[EUR][1000 genomes]
rs11162540	0.80[EUR][1000 genomes]
rs11162541	0.80[EUR][1000 genomes]
rs11587990	0.80[EUR][1000 genomes]
rs12120187	1.00[ASW][hapmap];0.91[CHB][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128384	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12403117	0.81[EUR][1000 genomes]
rs12409331	0.81[EUR][1000 genomes]
rs12409781	0.81[EUR][1000 genomes]
rs17395034	0.81[EUR][1000 genomes]
rs17398682	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17400419	0.84[JPT][hapmap]
rs1926901	0.82[EUR][1000 genomes]
rs1926902	0.81[EUR][1000 genomes]
rs1926903	0.81[EUR][1000 genomes]
rs1926904	0.81[EUR][1000 genomes]
rs1926905	0.81[EUR][1000 genomes]
rs58150654	0.81[EUR][1000 genomes]
rs58830966	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58921479	0.81[EUR][1000 genomes]
rs58945140	0.80[EUR][1000 genomes]
rs58993850	0.81[EUR][1000 genomes]
rs59409549	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60311076	0.81[EUR][1000 genomes]
rs61500835	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61613596	0.81[EUR][1000 genomes]
rs61681700	0.81[EUR][1000 genomes]
rs61769988	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61769992	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61769996	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61770023	0.81[EUR][1000 genomes]
rs61770024	0.81[EUR][1000 genomes]
rs6678067	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7546403	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs975986	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975987	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830315	chr1:79008443-79200591	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv871140	chr1:79095581-79155134	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs273250	IFI44	cis	parietal	SCAN
rs273250	IFI44	cis	cerebellum	SCAN
rs273250	GMIP	trans	cerebellum	SCAN
rs273250	ZZZ3	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79101400-79115400	Weak transcription	Left Ventricle	heart
2	chr1:79105000-79115400	Weak transcription	Psoas Muscle	Psoas
3	chr1:79105600-79115400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:79107600-79115600	Weak transcription	Aorta	Aorta
5	chr1:79107800-79115400	Weak transcription	Ovary	ovary
6	chr1:79111800-79115400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:79113400-79115400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:79113400-79115400	Weak transcription	Lung	lung
9	chr1:79113400-79115400	Weak transcription	Thymus	Thymus
10	chr1:79113600-79115400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:79113800-79115400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:79114200-79115400	Enhancers	Dnd41	blood
13	chr1:79114400-79115400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:79114600-79115400	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:79114800-79115400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr1:79114800-79115400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr1:79114800-79115400	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr1:79114800-79115400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:79114800-79115400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr1:79114800-79115400	Enhancers	Liver	Liver
21	chr1:79114800-79115400	Enhancers	Hela-S3	cervix
22	chr1:79115000-79115400	Enhancers	Primary B cells from peripheral blood	blood
23	chr1:79115000-79115400	Active TSS	Primary hematopoietic stem cells	blood
24	chr1:79115000-79115400	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr1:79115000-79115400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:79115000-79115400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr1:79115000-79115400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr1:79115000-79115400	Weak transcription	Adipose Nuclei	Adipose
29	chr1:79115000-79115400	Enhancers	Brain Hippocampus Middle	brain
30	chr1:79115000-79115400	Enhancers	Brain Substantia Nigra	brain
31	chr1:79115000-79115400	Enhancers	Colon Smooth Muscle	Colon
32	chr1:79115000-79115400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr1:79115000-79115400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:79115000-79115400	Enhancers	Fetal Brain Male	brain
35	chr1:79115000-79115400	Enhancers	HUVEC	blood vessel
36	chr1:79115000-79115400	Enhancers	Osteobl	bone
37	chr1:79115000-79115600	Enhancers	Small Intestine	intestine
38	chr1:79115000-79116400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:79115000-79117000	Active TSS	Brain Anterior Caudate	brain
40	chr1:79115000-79117600	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr1:79115000-79118200	Active TSS	Stomach Smooth Muscle	stomach
42	chr1:79115000-79118600	Active TSS	Right Atrium	heart
43	chr1:79115200-79115400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:79115200-79115400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:79115200-79115400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr1:79115200-79115400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:79115200-79115400	Weak transcription	Brain Germinal Matrix	brain
48	chr1:79115200-79115400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:79115200-79115400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:79115200-79115400	Enhancers	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links