Variant report

Variant	rs12463334
Chromosome Location	chr19:40169328-40169329
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	FAM48A	chr19:40169319-40169395	GM12878	blood:	n/a	n/a
2	MTA3	chr19:40168891-40170844	GM12878	blood:	n/a	n/a
3	RAD21	chr19:40169241-40169454	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr19:40169235-40169517	GM12878	blood:	n/a	n/a
5	TBL1XR1	chr19:40169272-40170547	GM12878	blood:	n/a	n/a
6	NFIC	chr19:40168553-40170977	GM12878	blood:	n/a	n/a
7	PAX5	chr19:40169111-40171253	GM12878	blood:	n/a	chr19:40170203-40170212
8	CTCF	chr19:40169220-40169370	HepG2	liver:	n/a	n/a
9	CTCF	chr19:40169262-40169449	GM12892	blood:	n/a	n/a
10	RAD21	chr19:40169192-40169505	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:40168990-40172822	GM12878	blood:	n/a	n/a
12	WRNIP1	chr19:40169125-40170937	GM12878	blood:	n/a	n/a
13	RAD21	chr19:40169227-40170522	GM12878	blood:	n/a	chr19:40169959-40169969 chr19:40169959-40169971
14	RAD21	chr19:40169187-40169504	HepG2	liver:	n/a	n/a
15	POLR2A	chr19:40169120-40172570	GM12878	blood:	n/a	n/a
16	CTCF	chr19:40169320-40169470	HepG2	liver:	n/a	n/a
17	EBF1	chr19:40168815-40171812	GM12878	blood:	n/a	n/a
18	STAT1	chr19:40169283-40169453	GM12878	blood:	n/a	n/a
19	CHD2	chr19:40169141-40171016	GM12878	blood:	n/a	n/a
20	CTCF	chr19:40169210-40169547	GM12878	blood:	n/a	n/a
21	PML	chr19:40169064-40170954	GM12878	blood:	n/a	chr19:40170206-40170214
22	ATF2	chr19:40169169-40171721	GM12878	blood:	n/a	n/a
23	CTCF	chr19:40169220-40169370	GM12873	blood:	n/a	n/a
24	POLR2A	chr19:40169083-40172673	GM12878	blood:	n/a	n/a
25	MTA3	chr19:40168531-40172519	GM12878	blood:	n/a	n/a
26	BRCA1	chr19:40169254-40169347	GM12878	blood:	n/a	n/a
27	CTCF	chr19:40169283-40169415	GM19240	blood:	n/a	n/a
28	STAT5A	chr19:40169134-40172621	GM12878	blood:	n/a	chr19:40172551-40172563 chr19:40169874-40169885 chr19:40172037-40172049 chr19:40170203-40170214
29	MXI1	chr19:40169202-40170872	GM12878	blood:	n/a	n/a
30	RAD21	chr19:40169270-40169423	HepG2	liver:	n/a	n/a
31	CTCF	chr19:40169240-40169390	HEK293	kidney:	n/a	n/a
32	SMC3	chr19:40169271-40171110	GM12878	blood:	n/a	n/a
33	CTCF	chr19:40169320-40169470	GM12873	blood:	n/a	n/a
34	CTCF	chr19:40169240-40169390	GM12873	blood:	n/a	n/a
35	CTCF	chr19:40169297-40169430	GM19238	blood:	n/a	n/a
36	RAD21	chr19:40169209-40169476	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr19:40169276-40169455	HepG2	liver:	n/a	n/a
38	MAX	chr19:40169288-40170797	GM12878	blood:	n/a	n/a
39	POLR2A	chr19:40169177-40169389	GM12878	blood:	n/a	n/a
40	NFATC1	chr19:40169041-40171846	GM12878	blood:	n/a	n/a
41	RUNX3	chr19:40169319-40171684	GM12878	blood:	n/a	n/a
42	CTCF	chr19:40169298-40169448	HepG2	liver:	n/a	n/a
43	CUX1	chr19:40169025-40171357	GM12878	blood:	n/a	chr19:40171034-40171043
44	MAZ	chr19:40169244-40170578	GM12878	blood:	n/a	n/a
45	CTCF	chr19:40169260-40169410	GM12865	blood:	n/a	n/a
46	CTCF	chr19:40169320-40169470	A549	lung:	n/a	n/a
47	RAD21	chr19:40169181-40169538	HepG2	liver:	n/a	n/a
48	CTCF	chr19:40169301-40169429	GM12878	blood:	n/a	n/a
49	POLR2A	chr19:40169221-40172689	GM18505	blood:	n/a	n/a
50	CTCF	chr19:40169278-40169430	GM12891	blood:	n/a	n/a

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: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs12463262	0.82[LWK][hapmap]

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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12463334	SAE1	cis	parietal	SCAN
rs12463334	CCDC61	cis	cerebellum	SCAN
rs12463334	CEACAM8	cis	cerebellum	SCAN
rs12463334	SEPW1	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40162600-40169600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:40166200-40169600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr19:40166200-40169600	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr19:40167400-40169600	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr19:40168000-40169800	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr19:40168200-40170000	Enhancers	Fetal Muscle Leg	muscle
7	chr19:40168200-40170400	Enhancers	Placenta	Placenta
8	chr19:40168400-40170200	Enhancers	Psoas Muscle	Psoas
9	chr19:40168400-40170600	Enhancers	Left Ventricle	heart
10	chr19:40168400-40170600	Enhancers	HepG2	liver
11	chr19:40168400-40171200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr19:40168600-40169400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr19:40168600-40169600	Enhancers	Duodenum Mucosa	Duodenum
14	chr19:40168600-40169800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr19:40168600-40169800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr19:40168600-40169800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr19:40168600-40170000	Enhancers	Gastric	stomach
18	chr19:40168600-40170400	Enhancers	Brain Anterior Caudate	brain
19	chr19:40168600-40170600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:40168600-40170600	Enhancers	Adipose Nuclei	Adipose
21	chr19:40168600-40170600	Enhancers	Lung	lung
22	chr19:40168600-40170600	Enhancers	Pancreas	Pancrea
23	chr19:40168600-40170600	Enhancers	Right Ventricle	heart
24	chr19:40168600-40170800	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr19:40168600-40171600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:40168600-40172600	Flanking Active TSS	GM12878-XiMat	blood
27	chr19:40168800-40169800	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr19:40168800-40169800	Weak transcription	Esophagus	oesophagus
29	chr19:40168800-40170800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr19:40168800-40171200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr19:40169000-40169800	Enhancers	Fetal Lung	lung
32	chr19:40169000-40169800	Enhancers	Small Intestine	intestine
33	chr19:40169000-40170200	Weak transcription	Colonic Mucosa	Colon
34	chr19:40169000-40170400	Enhancers	Colon Smooth Muscle	Colon
35	chr19:40169000-40171400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:40169200-40169400	Enhancers	Fetal Muscle Trunk	muscle
37	chr19:40169200-40169600	Enhancers	Liver	Liver
38	chr19:40169200-40169800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr19:40169200-40169800	Enhancers	Brain Substantia Nigra	brain

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