Variant report

Variant	rs553381359
Chromosome Location	chr1:209929955-209929956
allele	-/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	YY1	chr1:209929953-209930266	GM12891	blood:	n/a	chr1:209930105-209930114
2	POLR2A	chr1:209929084-209933092	GM18505	blood:	n/a	n/a
3	RCOR1	chr1:209928960-209930409	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:209928692-209932543	GM12891	blood:	n/a	n/a
5	POLR2A	chr1:209929004-209931083	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:209929899-209930355	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:209929113-209930511	HL-60	blood:	n/a	n/a
8	PML	chr1:209929099-209930052	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:209928989-209931083	GM12892	blood:	n/a	n/a
10	POLR2A	chr1:209929135-209930430	GM12891	blood:	n/a	n/a
11	EBF1	chr1:209929168-209930514	GM12878	blood:	n/a	chr1:209929739-209929748
12	POLR2A	chr1:209929144-209930769	GM12878	blood:	n/a	n/a
13	WRNIP1	chr1:209929394-209931411	GM12878	blood:	n/a	n/a
14	TAF1	chr1:209929877-209930280	GM12878	blood:	n/a	n/a
15	RELA	chr1:209928787-209930749	GM19099	blood:	n/a	chr1:209928807-209928816 chr1:209928807-209928816
16	SPI1	chr1:209929945-209930685	HL-60	blood:	n/a	chr1:209930342-209930355
17	POLR2A	chr1:209929032-209933590	GM12878	blood:	n/a	n/a
18	SPI1	chr1:209929888-209930584	GM12891	blood:	n/a	chr1:209930342-209930355
19	RUNX3	chr1:209928960-209930858	GM12878	blood:	n/a	chr1:209929212-209929221 chr1:209929212-209929221
20	POLR2A	chr1:209929922-209930447	GM12878	blood:	n/a	n/a
21	RUNX3	chr1:209928948-209930753	GM12878	blood:	n/a	chr1:209929212-209929221 chr1:209929212-209929221
22	POLR2A	chr1:209929143-209930855	GM12892	blood:	n/a	n/a
23	TBL1XR1	chr1:209929010-209930486	GM12878	blood:	n/a	n/a
24	TBP	chr1:209929015-209930614	GM12878	blood:	n/a	n/a
25	EBF1	chr1:209929234-209930686	GM12878	blood:	n/a	chr1:209929739-209929748
26	ELF1	chr1:209929889-209930355	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:209929141-209930623	GM15510	blood:	n/a	n/a
28	BHLHE40	chr1:209929950-209930349	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:209929232-209930682	GM12878	blood:	n/a	n/a
30	RELA	chr1:209928660-209930846	GM18951	blood:	n/a	chr1:209928807-209928816 chr1:209928807-209928816
31	CTCF	chr1:209929820-209929970	GM12873	blood:	n/a	n/a
32	POLR2A	chr1:209929926-209930438	GM12878	blood:	n/a	n/a
33	YY1	chr1:209929865-209930350	GM12892	blood:	n/a	chr1:209930105-209930114
34	POLR2A	chr1:209929761-209930728	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:209929903-209930613	GM12891	blood:	n/a	n/a
36	MAX	chr1:209929171-209930896	NB4	blood:	n/a	n/a
37	POLR2A	chr1:209929893-209930607	GM12891	blood:	n/a	n/a
38	MAX	chr1:209928994-209930579	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:209929034-209930872	GM18526	blood:	n/a	n/a
40	MYC	chr1:209929894-209930631	NB4	blood:	n/a	n/a
41	IKZF1	chr1:209928708-209930301	GM12878	blood:	n/a	chr1:209929687-209929699 chr1:209928803-209928815
42	POLR2A	chr1:209929250-209930593	GM12892	blood:	n/a	n/a
43	YY1	chr1:209929920-209930276	GM12892	blood:	n/a	chr1:209930105-209930114
44	GATA1	chr1:209929098-209930206	PBDE	blood:	n/a	chr1:209929895-209929904
45	MTA3	chr1:209929043-209930489	GM12878	blood:	n/a	n/a
46	NFIC	chr1:209928871-209930425	GM12878	blood:	n/a	n/a
47	MXI1	chr1:209929247-209930664	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:209929194-209930847	GM19193	blood:	n/a	n/a
49	POLR2A	chr1:209929183-209930965	GM12892	blood:	n/a	n/a
50	YY1	chr1:209929898-209930225	K562	blood:	n/a	chr1:209930105-209930114

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRAF3IP3-1	chr1:209929911-209930068	NONHSAT009231

Variant related genes	Relation type
TRAF3IP3	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1001588	chr1:209908876-209938243	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209921400-209930000	Weak transcription	Right Ventricle	heart
2	chr1:209921800-209930000	Weak transcription	Stomach Mucosa	stomach
3	chr1:209921800-209940800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:209921800-209942000	Weak transcription	Pancreas	Pancrea
5	chr1:209922400-209931200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:209928600-209932000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr1:209928600-209932200	Flanking Active TSS	GM12878-XiMat	blood
8	chr1:209928800-209930400	Flanking Active TSS	Dnd41	blood
9	chr1:209928800-209931000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr1:209928800-209932200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr1:209928800-209932400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr1:209929000-209931200	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr1:209929000-209931800	Active TSS	Duodenum Mucosa	Duodenum
14	chr1:209929000-209932000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr1:209929000-209932200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:209929000-209932200	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr1:209929000-209932400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:209929000-209932800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:209929200-209930800	Active TSS	Primary T cells from cord blood	blood
20	chr1:209929200-209931200	Flanking Active TSS	Primary B cells from peripheral blood	blood
21	chr1:209929200-209931400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:209929200-209931400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr1:209929400-209930000	Enhancers	Gastric	stomach
24	chr1:209929400-209930200	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
25	chr1:209929400-209930400	Active TSS	Thymus	Thymus
26	chr1:209929400-209930800	Active TSS	Fetal Thymus	thymus
27	chr1:209929400-209931000	Active TSS	Primary T cells fromperipheralblood	blood
28	chr1:209929400-209931000	Active TSS	Liver	Liver
29	chr1:209929400-209931000	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr1:209929400-209931200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:209929400-209931200	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr1:209929400-209931200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:209929400-209931400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr1:209929400-209931400	Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr1:209929400-209931400	Active TSS	Colonic Mucosa	Colon
36	chr1:209929400-209931800	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr1:209929400-209931800	Active TSS	Rectal Smooth Muscle	rectum
38	chr1:209929600-209930000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:209929600-209930000	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr1:209929600-209930400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:209929600-209930400	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr1:209929600-209930400	Enhancers	Lung	lung
43	chr1:209929600-209930600	Active TSS	Brain Hippocampus Middle	brain
44	chr1:209929600-209930800	Active TSS	Small Intestine	intestine
45	chr1:209929600-209931000	Active TSS	Esophagus	oesophagus
46	chr1:209929600-209931000	Active TSS	Spleen	Spleen
47	chr1:209929600-209931200	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr1:209929600-209931400	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr1:209929800-209930000	Active TSS	Fetal Intestine Small	intestine
50	chr1:209929800-209930000	Flanking Active TSS	Placenta	Placenta

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