Variant report

Variant	rs62119913
Chromosome Location	chr19:40170553-40170554
allele	C/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	RELA	chr19:40169621-40171019	GM18951	blood:	n/a	n/a
2	MTA3	chr19:40168891-40170844	GM12878	blood:	n/a	n/a
3	SP1	chr19:40169668-40170729	GM12878	blood:	n/a	chr19:40169958-40169972 chr19:40169815-40169824
4	POLR2A	chr19:40169482-40171648	GM12892	blood:	n/a	n/a
5	NFIC	chr19:40169476-40170857	GM12878	blood:	n/a	n/a
6	ZNF384	chr19:40170413-40170670	GM12878	blood:	n/a	n/a
7	MEF2A	chr19:40169620-40170723	GM12878	blood:	n/a	n/a
8	TCF12	chr19:40170403-40170832	GM12878	blood:	n/a	n/a
9	RCOR1	chr19:40169355-40170731	GM12878	blood:	n/a	n/a
10	NFIC	chr19:40168553-40170977	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:40169650-40171556	GM12892	blood:	n/a	n/a
12	BCL3	chr19:40170081-40170842	GM12878	blood:	n/a	n/a
13	PAX5	chr19:40169111-40171253	GM12878	blood:	n/a	chr19:40170203-40170212
14	ELK1	chr19:40170445-40170698	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:40168990-40172822	GM12878	blood:	n/a	n/a
16	TCF12	chr19:40169727-40170735	GM12878	blood:	n/a	n/a
17	WRNIP1	chr19:40169125-40170937	GM12878	blood:	n/a	n/a
18	IRF4	chr19:40169561-40170931	GM12878	blood:	n/a	n/a
19	CTCF	chr19:40170525-40170592	GM19239	blood:	n/a	n/a
20	STAT5A	chr19:40169635-40172036	GM12878	blood:	n/a	chr19:40169874-40169885 chr19:40170203-40170214
21	PAX5	chr19:40170087-40170561	GM12878	blood:	n/a	chr19:40170203-40170212
22	TCF3	chr19:40170327-40170837	GM12878	blood:	n/a	chr19:40170481-40170490 chr19:40170625-40170638
23	POLR2A	chr19:40169545-40171336	GM12878	blood:	n/a	n/a
24	CHD1	chr19:40169671-40171710	GM12878	blood:	n/a	n/a
25	STAT1	chr19:40169669-40170704	GM12878	blood:	n/a	chr19:40169874-40169885 chr19:40170203-40170214
26	BATF	chr19:40169465-40170751	GM12878	blood:	n/a	n/a
27	BCL11A	chr19:40169661-40170751	GM12878	blood:	n/a	n/a
28	POU2F2	chr19:40169756-40170872	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:40169648-40170882	GM12891	blood:	n/a	n/a
30	EP300	chr19:40169360-40171688	GM12878	blood:	n/a	chr19:40171353-40171367
31	PBX3	chr19:40170208-40170562	GM12878	blood:	n/a	n/a
32	CEBPB	chr19:40169429-40170617	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:40169120-40172570	GM12878	blood:	n/a	n/a
34	POU2F2	chr19:40169535-40171687	GM12878	blood:	n/a	chr19:40171354-40171376 chr19:40171361-40171371 chr19:40171023-40171037
35	RUNX3	chr19:40169498-40171475	GM12878	blood:	n/a	n/a
36	POLR2A	chr19:40169571-40171671	GM12891	blood:	n/a	n/a
37	NFATC1	chr19:40169430-40171167	GM12878	blood:	n/a	n/a
38	POLR2A	chr19:40169508-40171352	GM12892	blood:	n/a	n/a
39	RELA	chr19:40169507-40171055	GM10847	blood:	n/a	n/a
40	YY1	chr19:40169588-40170826	GM12878	blood:	n/a	n/a
41	EBF1	chr19:40168815-40171812	GM12878	blood:	n/a	n/a
42	PML	chr19:40169711-40170792	GM12878	blood:	n/a	chr19:40170206-40170214
43	POLR2A	chr19:40169378-40171658	GM12892	blood:	n/a	n/a
44	CHD2	chr19:40169141-40171016	GM12878	blood:	n/a	n/a
45	PML	chr19:40169064-40170954	GM12878	blood:	n/a	chr19:40170206-40170214
46	EP300	chr19:40169694-40170703	GM12878	blood:	n/a	n/a
47	ATF2	chr19:40169169-40171721	GM12878	blood:	n/a	n/a
48	POLR2A	chr19:40169695-40171532	GM19193	blood:	n/a	n/a
49	POLR2A	chr19:40169664-40171222	GM15510	blood:	n/a	n/a
50	PAX5	chr19:40170077-40170797	GM12878	blood:	n/a	chr19:40170203-40170212

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40168776..40170659-chr19:40171070..40173926,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226025	TF binding region
ENSG00000226025	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs62119908	1.00[EUR][1000 genomes]
rs62119911	1.00[EUR][1000 genomes]
rs62119912	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057361	chr19:40123868-40310996	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv2482	chr19:40125797-40170766	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3413868	chr19:40130700-40184720	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1061361	chr19:40131820-40310996	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv579511	chr19:40132825-40310497	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1062394	chr19:40133229-40310186	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv544004	chr19:40133229-40310186	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv3355956	chr19:40135051-40188792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	esv3998	chr19:40135120-40188646	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	esv3397881	chr19:40150495-40199437	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv1059691	chr19:40168862-40306373	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv544005	chr19:40168862-40306373	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv960763	chr19:40168890-40177573	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40168400-40170600	Enhancers	Left Ventricle	heart
2	chr19:40168400-40170600	Enhancers	HepG2	liver
3	chr19:40168400-40171200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr19:40168600-40170600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:40168600-40170600	Enhancers	Adipose Nuclei	Adipose
6	chr19:40168600-40170600	Enhancers	Lung	lung
7	chr19:40168600-40170600	Enhancers	Pancreas	Pancrea
8	chr19:40168600-40170600	Enhancers	Right Ventricle	heart
9	chr19:40168600-40170800	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr19:40168600-40171600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:40168600-40172600	Flanking Active TSS	GM12878-XiMat	blood
12	chr19:40168800-40170800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:40168800-40171200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr19:40169000-40171400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:40169600-40170600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr19:40169600-40170600	Enhancers	Fetal Kidney	kidney
17	chr19:40169600-40170800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr19:40169600-40170800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:40169600-40170800	Enhancers	Spleen	Spleen
20	chr19:40169800-40170600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr19:40169800-40170600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr19:40169800-40171000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr19:40170000-40170600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr19:40170000-40170800	Active TSS	Fetal Muscle Trunk	muscle
25	chr19:40170000-40171000	Active TSS	Fetal Muscle Leg	muscle
26	chr19:40170000-40184600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:40170200-40170600	Enhancers	Duodenum Mucosa	Duodenum
28	chr19:40170200-40170600	Flanking Active TSS	Psoas Muscle	Psoas
29	chr19:40170200-40170800	Enhancers	Colonic Mucosa	Colon
30	chr19:40170400-40170600	Enhancers	Small Intestine	intestine
31	chr19:40170400-40171000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr19:40170400-40171000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr19:40170400-40171400	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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