Variant report

Variant	rs2280525
Chromosome Location	chr3:195974181-195974182
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	GABPA	chr3:195973815-195974294	HL-60	blood:	n/a	n/a
2	POLR2A	chr3:195973685-195974244	U87	brain:	n/a	n/a
3	FOS	chr3:195973802-195974271	MCF10A-Er-Src	breast:	n/a	n/a
4	SPI1	chr3:195973840-195974283	HL-60	blood:	n/a	n/a
5	STAT3	chr3:195973416-195974297	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr3:195973456-195974400	HL-60	blood:	n/a	n/a
7	POLR2A	chr3:195973664-195974323	U87	brain:	n/a	n/a
8	FOS	chr3:195973685-195974201	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr3:195973408-195974406	HL-60	blood:	n/a	n/a
10	FOS	chr3:195973724-195974263	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr3:195973818-195974244	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:195952863..195955052-chr3:195973498..195975966,2	K562	blood:
2	chr3:195958884..195960424-chr3:195972113..195974415,2	K562	blood:

Variant related genes	Relation type
ENSG00000228028	TF binding region
ENSG00000163959	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11185523	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs12053980	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12490786	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12632013	1.00[CEU][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13083065	0.83[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs35270876	0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs56107869	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56152446	0.88[ASN][1000 genomes]
rs58820816	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6771755	0.96[ASN][1000 genomes]
rs73084688	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73084691	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73084695	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73086649	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7648600	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9714228	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv1008512	chr3:195709662-195974936	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
7	nsv1009105	chr3:195769609-195984388	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
9	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
10	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
11	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
12	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
13	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
14	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
15	nsv878178	chr3:195929268-195998451	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers 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	14 gene(s)	inside rSNPs	diseases
16	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
17	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
18	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
19	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
20	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
21	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
22	esv3341217	chr3:195972755-195975953	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
23	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2280525	PCYT1A	cis	Liver	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195959600-195978200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:195962400-195977000	Strong transcription	Fetal Stomach	stomach
3	chr3:195962400-195979400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:195964000-195975000	Strong transcription	Fetal Brain Female	brain
5	chr3:195965200-195994200	Weak transcription	A549	lung
6	chr3:195965600-195975800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:195965800-195976600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:195965800-196012400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:195967000-195975200	Strong transcription	Aorta	Aorta
10	chr3:195967200-195988600	Strong transcription	Fetal Intestine Small	intestine
11	chr3:195967400-195975600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:195968400-195976400	Strong transcription	Spleen	Spleen
13	chr3:195968800-195993400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:195969200-195978200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:195969600-195974200	Weak transcription	Psoas Muscle	Psoas
16	chr3:195969600-195974400	Weak transcription	Fetal Kidney	kidney
17	chr3:195969600-195982400	Weak transcription	Fetal Heart	heart
18	chr3:195969600-196012400	Weak transcription	Fetal Brain Male	brain
19	chr3:195969800-195974200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:195969800-195974200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:195970800-195975200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:195971000-195975400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:195971000-195975400	Strong transcription	Lung	lung
24	chr3:195971200-195979600	Strong transcription	Fetal Muscle Leg	muscle
25	chr3:195971600-195978400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr3:195971800-195974600	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr3:195971800-195975200	Strong transcription	Rectal Smooth Muscle	rectum
28	chr3:195971800-195976000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:195972000-195974600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:195972000-195975200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:195972000-195975200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:195972000-195975200	Strong transcription	HSMMtube	muscle
33	chr3:195972000-195975400	Strong transcription	K562	blood
34	chr3:195972200-195974200	Strong transcription	NH-A	brain
35	chr3:195972200-195974400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:195972200-195974600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:195972200-195974800	Strong transcription	Fetal Lung	lung
38	chr3:195972200-195975000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:195972200-195975000	Strong transcription	Fetal Thymus	thymus
40	chr3:195972200-195975000	Strong transcription	Stomach Smooth Muscle	stomach
41	chr3:195972200-195975000	Strong transcription	GM12878-XiMat	blood
42	chr3:195972200-195975200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:195972200-195975200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:195972200-195975200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:195972200-195975200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr3:195972200-195975200	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:195972200-195975200	Strong transcription	Adipose Nuclei	Adipose
48	chr3:195972200-195975200	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr3:195972200-195975200	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:195972200-195975200	Strong transcription	Fetal Muscle Trunk	muscle

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