Variant report

Variant	rs2288509
Chromosome Location	chr19:42392310-42392311
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	STAT5A	chr19:42390913-42392313	GM12878	blood:	n/a	chr19:42391744-42391756 chr19:42391630-42391637
2	POLR2A	chr19:42392021-42392345	GM12891	blood:	n/a	n/a
3	CTCF	chr19:42391573-42392398	HCT-116	colon:	n/a	chr19:42391953-42391971 chr19:42391959-42391968 chr19:42391955-42391968 chr19:42391955-42391968 chr19:42391956-42391966
4	POLR2A	chr19:42392285-42392383	MCF-7	breast:	n/a	n/a
5	MYBL2	chr19:42391719-42392360	HepG2	liver:	n/a	n/a
6	YY1	chr19:42391756-42392390	HepG2	liver:	n/a	chr19:42391826-42391837
7	POLR2A	chr19:42391654-42392351	HCT-116	colon:	n/a	n/a
8	POLR2A	chr19:42390762-42392615	GM12892	blood:	n/a	n/a
9	EGR1	chr19:42391497-42392509	HCT-116	colon:	n/a	chr19:42391923-42391936 chr19:42391641-42391650 chr19:42391951-42391965 chr19:42392012-42392026 chr19:42391918-42391940
10	POLR2A	chr19:42390925-42392449	GM12878	blood:	n/a	n/a
11	EGR1	chr19:42391568-42392545	HCT-116	colon:	n/a	chr19:42391923-42391936 chr19:42391641-42391650 chr19:42391951-42391965 chr19:42392012-42392026 chr19:42391918-42391940
12	FOXA1	chr19:42391721-42392330	HepG2	liver:	n/a	n/a
13	HDAC2	chr19:42391775-42392433	HepG2	liver:	n/a	chr19:42392037-42392046
14	RAD21	chr19:42391780-42392324	HepG2	liver:	n/a	chr19:42391792-42391805 chr19:42391951-42391970 chr19:42391954-42391967 chr19:42391955-42391965
15	FOXA1	chr19:42391809-42392332	HepG2	liver:	n/a	n/a
16	POLR2A	chr19:42389937-42394570	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:42391355-42392325	GM12878	blood:	n/a	n/a
18	FOXA2	chr19:42391540-42392508	HepG2	liver:	n/a	n/a
19	TCF12	chr19:42391909-42392337	ECC-1	luminal epithelium:	n/a	chr19:42392060-42392068 chr19:42392052-42392059 chr19:42392037-42392046
20	POLR2A	chr19:42391930-42392514	K562	blood:	n/a	n/a
21	NRF1	chr19:42392268-42392371	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:42390927-42392345	GM18505	blood:	n/a	n/a
23	POLR2A	chr19:42390846-42392476	GM12892	blood:	n/a	n/a
24	RUNX3	chr19:42390749-42392408	GM12878	blood:	n/a	n/a
25	NFIC	chr19:42391833-42392378	HepG2	liver:	n/a	n/a
26	POU2F2	chr19:42390888-42392321	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:42390244-42392330	GM12891	blood:	n/a	n/a
28	MTA3	chr19:42390605-42392477	GM12878	blood:	n/a	n/a
29	SIN3AK20	chr19:42391653-42392571	MCF-7	breast:	n/a	n/a
30	TCF12	chr19:42391686-42392364	ECC-1	luminal epithelium:	n/a	chr19:42392060-42392068 chr19:42392052-42392059 chr19:42392037-42392046
31	POLR2A	chr19:42391880-42392358	GM12891	blood:	n/a	n/a
32	HNF4G	chr19:42391738-42392317	HepG2	liver:	n/a	n/a
33	POLR2A	chr19:42390874-42392486	GM12878	blood:	n/a	n/a
34	HDAC2	chr19:42391881-42392460	MCF-7	breast:	n/a	chr19:42392037-42392046
35	RUNX3	chr19:42390931-42392418	GM12878	blood:	n/a	n/a
36	FOS	chr19:42391908-42392313	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr19:42391753-42392370	HepG2	liver:	n/a	n/a
38	FOSL2	chr19:42391779-42392342	HepG2	liver:	n/a	n/a
39	TBL1XR1	chr19:42390983-42392466	GM12878	blood:	n/a	n/a
40	SP1	chr19:42391818-42392387	HepG2	liver:	n/a	chr19:42391952-42391966 chr19:42391951-42391963 chr19:42391953-42391962 chr19:42391951-42391963
41	POLR2A	chr19:42391033-42392437	GM12878	blood:	n/a	n/a
42	ZEB1	chr19:42391764-42392336	HepG2	liver:	n/a	n/a
43	CTCF	chr19:42392180-42392330	GM12878	blood:	n/a	n/a
44	EP300	chr19:42391828-42392319	HepG2	liver:	n/a	n/a
45	CEBPD	chr19:42391790-42392331	HepG2	liver:	n/a	n/a
46	POLR2A	chr19:42390651-42392446	GM12892	blood:	n/a	n/a
47	FOXA1	chr19:42391829-42392322	HepG2	liver:	n/a	n/a
48	POLR2A	chr19:42389706-42394346	SK-N-MC	brain:	n/a	n/a
49	POLR2A	chr19:42392028-42392345	H1-hESC	embryonic stem cell:	n/a	n/a
50	FOXA2	chr19:42391809-42392355	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42390528..42393391-chr19:42425919..42428755,3	MCF-7	breast:
2	chr19:42392091..42393958-chr19:42398936..42401032,2	MCF-7	breast:
3	chr19:42385706..42396512-chr19:42423854..42433641,19	K562	blood:
4	chr19:42390140..42393678-chr19:42394261..42398306,6	K562	blood:
5	chr19:42391577..42392478-chr19:42455568..42456267,3	MCF-7	breast:
6	chr19:42390499..42394130-chr19:42395488..42398499,5	MCF-7	breast:
7	chr19:42392209..42393764-chr19:42436323..42438762,2	MCF-7	breast:
8	chr19:42391492..42392504-chr19:42461709..42462601,3	MCF-7	breast:
9	chr19:42384855..42393410-chr19:42428364..42439251,22	K562	blood:
10	chr19:42390553..42393119-chr19:42395224..42396776,2	MCF-7	breast:
11	chr19:42391908..42392858-chr19:42455448..42456435,2	K562	blood:
12	chr19:42387951..42392334-chr19:42459610..42463737,7	MCF-7	breast:
13	chr19:42390344..42392993-chr19:42439270..42441134,2	MCF-7	breast:
14	chr19:42385266..42389164-chr19:42392215..42397025,5	MCF-7	breast:
15	chr19:42362804..42368897-chr19:42386582..42393421,16	MCF-7	breast:
16	chr19:42392300..42393961-chr19:42403075..42405096,2	K562	blood:
17	chr19:42390993..42392677-chr19:42461992..42463492,2	K562	blood:
18	chr19:42390448..42392513-chr19:42434205..42436040,2	MCF-7	breast:

Variant related genes	Relation type
ARHGEF1	TF binding region
ENSG00000105372	Chromatin interaction
ENSG00000076928	Chromatin interaction
ENSG00000105404	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10401189	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10401937	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10402667	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10403081	0.84[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10417495	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10419314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11878536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11878555	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs12104228	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16975619	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288510	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2288511	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2288512	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2303798	0.94[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28396197	0.82[AMR][1000 genomes]
rs28521795	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28706300	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3745222	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6509003	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs717225	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7252790	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7252800	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7253691	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[ASN][1000 genomes]
rs73550603	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73550610	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8109784	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8109959	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8110305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8113339	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8113686	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs891169	0.88[ASN][1000 genomes]
rs891170	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs891171	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs891172	0.84[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription 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	92 gene(s)	inside rSNPs	diseases
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42389000-42392400	Enhancers	Pancreas	Pancrea
2	chr19:42389000-42396000	Weak transcription	Aorta	Aorta
3	chr19:42389000-42396000	Weak transcription	Ovary	ovary
4	chr19:42389200-42392400	Enhancers	Fetal Intestine Large	intestine
5	chr19:42389200-42392600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
6	chr19:42389200-42407200	Weak transcription	Fetal Kidney	kidney
7	chr19:42389200-42429200	Weak transcription	Right Atrium	heart
8	chr19:42389400-42392400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:42389400-42392400	Enhancers	Gastric	stomach
10	chr19:42389400-42392600	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr19:42389400-42392800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr19:42389400-42393000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:42389400-42393600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:42389400-42398200	Weak transcription	Colon Smooth Muscle	Colon
15	chr19:42389400-42402000	Weak transcription	Psoas Muscle	Psoas
16	chr19:42389400-42406000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:42389400-42411400	Weak transcription	Fetal Brain Male	brain
18	chr19:42389800-42392400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr19:42389800-42392800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:42389800-42393000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:42389800-42409000	Strong transcription	Fetal Stomach	stomach
22	chr19:42390000-42392600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:42390200-42392400	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr19:42390200-42392400	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr19:42390200-42392800	Enhancers	NH-A	brain
26	chr19:42390400-42392400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:42390400-42392400	Enhancers	Fetal Lung	lung
28	chr19:42390400-42392600	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr19:42390400-42392600	Active TSS	Thymus	Thymus
30	chr19:42390400-42392800	Enhancers	Brain Angular Gyrus	brain
31	chr19:42390600-42392400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr19:42390600-42393200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr19:42390800-42392400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:42390800-42392400	Flanking Active TSS	HMEC	breast
35	chr19:42390800-42392600	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr19:42390800-42411200	Weak transcription	Hela-S3	cervix
37	chr19:42391000-42392400	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr19:42391000-42392400	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr19:42391000-42392400	Flanking Active TSS	Brain Hippocampus Middle	brain
40	chr19:42391000-42392600	Enhancers	H1 Cell Line	embryonic stem cell
41	chr19:42391000-42392600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:42391000-42392600	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr19:42391000-42392600	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr19:42391000-42392600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr19:42391000-42392600	Genic enhancers	Placenta	Placenta
46	chr19:42391000-42392800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:42391000-42393000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:42391000-42394000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
49	chr19:42391200-42392400	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr19:42391200-42392400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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