Variant report

Variant	rs2460719
Chromosome Location	chr3:100328017-100328018
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	CTCF	chr3:100327900-100328050	WERI-Rb-1	eye:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100325886..100329093-chr3:100426560..100431642,4	MCF-7	breast:

Variant related genes	Relation type
GPR128	TF binding region
ENSG00000114354	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10755119	0.88[CEU][hapmap]
rs10936276	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1144122	0.84[CEU][hapmap]
rs1144124	0.85[CEU][hapmap]
rs1144125	0.83[CEU][hapmap]
rs1144126	0.84[CEU][hapmap]
rs1145346	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1145348	0.85[CEU][hapmap]
rs1165264	0.85[CEU][hapmap]
rs11921801	0.88[CEU][hapmap]
rs11921907	0.85[CEU][hapmap]
rs12633554	0.88[ASN][1000 genomes]
rs12634495	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12636989	0.88[ASN][1000 genomes]
rs1471375	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1520650	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1520651	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1531772	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1676340	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1676343	0.92[CEU][hapmap]
rs1680508	0.88[ASN][1000 genomes]
rs16842463	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1718275	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915309	0.81[CEU][hapmap]
rs2046227	0.86[EUR][1000 genomes]
rs2246355	0.88[ASN][1000 genomes]
rs2317284	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2317285	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2449253	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3087787	0.81[CEU][hapmap]
rs3796276	0.81[CEU][hapmap]
rs3924054	0.88[JPT][hapmap]
rs4088588	0.85[CEU][hapmap]
rs4129205	0.84[CHB][hapmap]
rs4144968	0.85[CEU][hapmap]
rs4928070	0.84[CEU][hapmap]
rs58351812	0.83[ASN][1000 genomes]
rs586347	0.85[CEU][hapmap]
rs60544131	0.89[ASN][1000 genomes]
rs60938133	0.90[ASN][1000 genomes]
rs610854	0.84[CEU][hapmap]
rs61730367	0.88[ASN][1000 genomes]
rs6441383	0.85[CEU][hapmap]
rs6441384	0.84[CEU][hapmap]
rs66517733	0.88[ASN][1000 genomes]
rs6763086	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6767460	0.89[CEU][hapmap]
rs6770367	0.84[ASN][1000 genomes]
rs6770559	0.89[CEU][hapmap]
rs6779489	0.84[CEU][hapmap]
rs6780378	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6789364	0.85[CEU][hapmap]
rs694612	0.81[CEU][hapmap]
rs72914684	0.89[ASN][1000 genomes]
rs73143168	0.86[ASN][1000 genomes]
rs73145123	0.86[ASN][1000 genomes]
rs7426414	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7618197	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7622958	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7640289	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs900235	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9866111	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751965	chr3:100299310-100462527	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	esv2751966	chr3:100299310-100468500	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv2756284	chr3:100299329-100427937	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2752830	chr3:100299329-100442478	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv432464	chr3:100299329-100442478	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv2751967	chr3:100299329-100455139	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv2751968	chr3:100299329-100476713	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats 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
8	nsv432466	chr3:100299329-100476713	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv536667	chr3:100308355-100445857	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv460770	chr3:100310812-100433592	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv591150	chr3:100310812-100433592	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv2751969	chr3:100312499-100479384	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	esv2763708	chr3:100317928-100442509	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv591151	chr3:100322043-100433592	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	esv3462232	chr3:100323900-100329728	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
16	esv3462231	chr3:100323931-100329687	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
17	esv3462233	chr3:100323931-100329687	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
18	nsv1006559	chr3:100324275-100427937	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv877219	chr3:100324442-100400733	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv516418	chr3:100324442-100433592	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
21	nsv460771	chr3:100324442-100433592	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
22	nsv591152	chr3:100324442-100433592	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
23	nsv877220	chr3:100324442-100467018	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
24	nsv822201	chr3:100325319-100329560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
25	nsv1007742	chr3:100326173-100441716	Flanking Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
26	nsv1014117	chr3:100326173-100442478	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2460719	TFG	cis	multi-tissue	Pritchard

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100322800-100328200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:100322800-100328200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:100322800-100330200	Weak transcription	HepG2	liver
4	chr3:100323000-100328200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:100323000-100328200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:100323200-100328400	Weak transcription	HMEC	breast
7	chr3:100326000-100328400	Weak transcription	Stomach Mucosa	stomach
8	chr3:100327200-100328400	Enhancers	Fetal Intestine Small	intestine
9	chr3:100327600-100334200	Active TSS	Duodenum Mucosa	Duodenum
10	chr3:100327800-100328200	Enhancers	Fetal Thymus	thymus
11	chr3:100327800-100328600	Enhancers	Dnd41	blood
12	chr3:100327800-100328800	Enhancers	Primary T cells from cord blood	blood
13	chr3:100327800-100329000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr3:100327800-100329000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:100327800-100330200	Weak transcription	Liver	Liver
16	chr3:100328000-100328200	Enhancers	Colonic Mucosa	Colon
17	chr3:100328000-100328400	Flanking Active TSS	Fetal Intestine Large	intestine
18	chr3:100328000-100328400	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr3:100328000-100328600	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr3:100328000-100328600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:100328000-100328800	Enhancers	Primary hematopoietic stem cells	blood
22	chr3:100328000-100328800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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