Variant report

Variant	rs13097409
Chromosome Location	chr3:20167830-20167831
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	MAX	chr3:20167361-20167946	GM12878	blood:	n/a	chr3:20167807-20167816
2	NFATC1	chr3:20167171-20167895	GM12878	blood:	n/a	n/a
3	ZNF384	chr3:20167546-20167839	GM12878	blood:	n/a	n/a
4	NFIC	chr3:20167324-20167989	GM12878	blood:	n/a	n/a
5	RUNX3	chr3:20167249-20168039	GM12878	blood:	n/a	n/a
6	YY1	chr3:20167474-20167830	GM12891	blood:	n/a	n/a
7	IRF4	chr3:20167343-20167853	GM12878	blood:	n/a	n/a
8	ATF2	chr3:20167264-20167940	GM12878	blood:	n/a	n/a
9	CUX1	chr3:20167296-20167955	GM12878	blood:	n/a	n/a
10	BCLAF1	chr3:20167291-20167861	GM12878	blood:	n/a	n/a
11	NFIC	chr3:20167299-20168101	GM12878	blood:	n/a	n/a
12	SPI1	chr3:20167352-20167949	HL-60	blood:	n/a	chr3:20167651-20167664 chr3:20167650-20167663 chr3:20167620-20167633 chr3:20167653-20167662
13	YY1	chr3:20167376-20167841	GM12892	blood:	n/a	n/a
14	TCF3	chr3:20167336-20167889	GM12878	blood:	n/a	chr3:20167706-20167716
15	ELF1	chr3:20167363-20167844	GM12878	blood:	n/a	n/a
16	EP300	chr3:20167330-20167890	GM12878	blood:	n/a	chr3:20167636-20167645 chr3:20167617-20167631
17	FOXM1	chr3:20167244-20167913	GM12878	blood:	n/a	n/a
18	SMC3	chr3:20167407-20167871	GM12878	blood:	n/a	n/a
19	SPI1	chr3:20167106-20168181	GM12878	blood:	n/a	chr3:20167651-20167664 chr3:20167650-20167663 chr3:20167620-20167633 chr3:20167653-20167662
20	POLR2A	chr3:20167319-20167853	GM12892	blood:	n/a	n/a
21	SPI1	chr3:20167409-20167862	GM12878	blood:	n/a	chr3:20167651-20167664 chr3:20167650-20167663 chr3:20167620-20167633 chr3:20167653-20167662
22	PML	chr3:20167305-20167903	GM12878	blood:	n/a	n/a
23	MTA3	chr3:20167202-20167961	GM12878	blood:	n/a	n/a
24	PAX5	chr3:20167361-20167863	GM12891	blood:	n/a	chr3:20167654-20167663 chr3:20167617-20167626
25	PAX5	chr3:20167377-20167862	GM12878	blood:	n/a	chr3:20167654-20167663 chr3:20167617-20167626
26	BCLAF1	chr3:20167417-20167858	GM12878	blood:	n/a	n/a
27	CHD2	chr3:20167239-20167866	GM12878	blood:	n/a	n/a
28	ATF2	chr3:20167304-20167868	GM12878	blood:	n/a	n/a
29	SPI1	chr3:20167350-20167895	GM12891	blood:	n/a	chr3:20167651-20167664 chr3:20167650-20167663 chr3:20167620-20167633 chr3:20167653-20167662
30	BHLHE40	chr3:20167225-20167843	GM12878	blood:	n/a	n/a
31	CREB1	chr3:20167338-20167895	GM12878	blood:	n/a	n/a
32	TBL1XR1	chr3:20167367-20167941	GM12878	blood:	n/a	n/a
33	IRF4	chr3:20167287-20167910	GM12878	blood:	n/a	n/a
34	TBP	chr3:20167435-20167855	GM12878	blood:	n/a	n/a
35	PAX5	chr3:20167288-20167942	GM12878	blood:	n/a	chr3:20167654-20167663 chr3:20167617-20167626
36	YY1	chr3:20167393-20167878	GM12878	blood:	n/a	n/a
37	FOXM1	chr3:20167072-20168005	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
KAT2B	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11713069	1.00[ASN][1000 genomes]
rs12486167	1.00[LWK][hapmap]
rs13066876	1.00[ASN][1000 genomes]
rs13066923	1.00[ASN][1000 genomes]
rs13069629	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095743	1.00[ASN][1000 genomes]
rs13096876	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097157	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098588	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17180771	1.00[LWK][hapmap]
rs17627750	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17627906	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17627936	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17678713	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17796230	1.00[LWK][hapmap]
rs17796904	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17804451	1.00[ASN][1000 genomes]
rs34204839	1.00[ASN][1000 genomes]
rs34515517	1.00[ASN][1000 genomes]
rs34572705	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35424474	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35632245	1.00[ASN][1000 genomes]
rs35645247	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35659955	1.00[ASN][1000 genomes]
rs35776229	1.00[ASN][1000 genomes]
rs35841175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36029475	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3849533	1.00[LWK][hapmap]
rs3960789	1.00[ASN][1000 genomes]
rs41285061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241545	1.00[ASN][1000 genomes]
rs4858156	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858171	1.00[ASN][1000 genomes]
rs4858751	1.00[ASN][1000 genomes]
rs4858752	1.00[ASN][1000 genomes]
rs4858755	1.00[ASN][1000 genomes]
rs4858763	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858765	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55812129	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs71316246	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71316248	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71316249	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	15 gene(s)	inside rSNPs	diseases
4	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers 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 miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	esv1829018	chr3:20116077-20596244	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
12	esv1827700	chr3:20119716-20489086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	esv1830036	chr3:20121828-20278275	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
14	esv1830599	chr3:20121828-20375643	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	esv1828816	chr3:20136508-20389045	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
16	esv3394910	chr3:20150394-20203576	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
17	esv3334928	chr3:20150414-20203546	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
18	esv1832674	chr3:20152772-20605302	Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
19	esv1831853	chr3:20157077-20615273	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
20	esv1833208	chr3:20157077-20638228	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
21	esv2422249	chr3:20163608-20626956	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
22	esv1826144	chr3:20164282-20638228	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13097409	UBE2E2	cis	parietal	SCAN
rs13097409	SGOL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20116400-20194800	Weak transcription	NHDF-Ad	bronchial
2	chr3:20128200-20175800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:20135200-20173800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:20141200-20222400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:20142600-20189400	Weak transcription	Fetal Brain Male	brain
6	chr3:20147400-20169600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:20147600-20194200	Weak transcription	Dnd41	blood
8	chr3:20151000-20196800	Weak transcription	Stomach Mucosa	stomach
9	chr3:20151200-20179000	Weak transcription	Fetal Kidney	kidney
10	chr3:20151600-20175800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:20152000-20182800	Weak transcription	Colonic Mucosa	Colon
12	chr3:20152600-20175200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:20152800-20170200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:20152800-20175000	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr3:20152800-20176200	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr3:20153600-20169200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:20154000-20178400	Weak transcription	Psoas Muscle	Psoas
18	chr3:20157000-20178800	Weak transcription	HUVEC	blood vessel
19	chr3:20158000-20172400	Weak transcription	Fetal Brain Female	brain
20	chr3:20158800-20169200	Weak transcription	Spleen	Spleen
21	chr3:20159200-20201400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:20160200-20170200	Strong transcription	Primary T cells from cord blood	blood
23	chr3:20160200-20170200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:20160400-20169400	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:20160400-20171800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:20160400-20182000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:20160600-20175400	Strong transcription	Liver	Liver
28	chr3:20160600-20176000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:20160800-20169800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:20161000-20169200	Strong transcription	Left Ventricle	heart
31	chr3:20161000-20169800	Strong transcription	Stomach Smooth Muscle	stomach
32	chr3:20161000-20170000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:20161000-20173400	Strong transcription	Fetal Thymus	thymus
34	chr3:20161200-20171400	Strong transcription	Adipose Nuclei	Adipose
35	chr3:20162200-20183400	Weak transcription	Gastric	stomach
36	chr3:20162200-20184000	Weak transcription	Right Ventricle	heart
37	chr3:20162800-20169800	Strong transcription	Fetal Lung	lung
38	chr3:20162800-20183000	Weak transcription	Fetal Heart	heart
39	chr3:20162800-20198200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:20163400-20169800	Strong transcription	Fetal Muscle Leg	muscle
41	chr3:20163400-20170000	Strong transcription	Thymus	Thymus
42	chr3:20163400-20171400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:20163400-20171600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr3:20163400-20172000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:20163600-20170400	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:20164000-20169400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:20164000-20176200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:20164200-20169800	Strong transcription	Fetal Stomach	stomach
49	chr3:20164400-20168800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:20164400-20204400	Weak transcription	Small Intestine	intestine

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