Variant report

Variant	rs45624940
Chromosome Location	chr2:113931222-113931223
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	ELK1	chr2:113931156-113931748	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:113931026-113932042	HL-60	blood:	n/a	n/a
3	SPI1	chr2:113931077-113931697	GM12891	blood:	n/a	n/a
4	POLR2A	chr2:113930967-113935020	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:113931047-113933306	GM18505	blood:	n/a	n/a
6	POLR2A	chr2:113931220-113931798	K562	blood:	n/a	n/a
7	MYC	chr2:113930847-113932357	NB4	blood:	n/a	chr2:113931713-113931723
8	ATF2	chr2:113931152-113932065	GM12878	blood:	n/a	n/a
9	CEBPB	chr2:113931129-113931305	HepG2	liver:	n/a	chr2:113931134-113931145 chr2:113931132-113931143 chr2:113931134-113931145
10	CTCF	chr2:113931080-113931230	GM12874	blood:	n/a	n/a
11	HEY1	chr2:113931185-113931785	K562	blood:	n/a	n/a
12	RUNX3	chr2:113931019-113933669	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:113931075-113934128	GM19193	blood:	n/a	n/a
14	POLR2A	chr2:113931101-113933233	GM12878	blood:	n/a	n/a
15	NFIC	chr2:113931189-113931757	GM12878	blood:	n/a	n/a
16	CTCF	chr2:113931140-113931290	GM12870	blood:	n/a	n/a
17	NR2F2	chr2:113930887-113931691	K562	blood:	n/a	n/a
18	POLR2A	chr2:113931013-113931952	HL-60	blood:	n/a	n/a
19	POLR2A	chr2:113931149-113932041	K562	blood:	n/a	n/a
20	CTCF	chr2:113931120-113931270	GM12871	blood:	n/a	n/a
21	POLR2A	chr2:113931131-113931989	GM12892	blood:	n/a	n/a
22	HMGN3	chr2:113931196-113932083	K562	blood:	n/a	n/a
23	MAX	chr2:113931011-113931928	NB4	blood:	n/a	chr2:113931713-113931723
24	CTCF	chr2:113931080-113931230	GM12872	blood:	n/a	n/a
25	MYC	chr2:113931120-113932192	K562	blood:	n/a	chr2:113931713-113931723
26	MXI1	chr2:113931063-113932457	GM12878	blood:	n/a	chr2:113931726-113931735
27	POLR2A	chr2:113930698-113934407	GM12878	blood:	n/a	n/a
28	RCOR1	chr2:113930812-113931721	K562	blood:	n/a	n/a
29	CEBPB	chr2:113931000-113931273	K562	blood:	n/a	chr2:113931134-113931145 chr2:113931132-113931143 chr2:113931134-113931145
30	POLR2A	chr2:113931191-113932013	K562	blood:	n/a	n/a
31	FOXM1	chr2:113931131-113931842	GM12878	blood:	n/a	n/a
32	RELA	chr2:113930935-113931800	GM18951	blood:	n/a	n/a
33	SPI1	chr2:113931070-113931720	GM12891	blood:	n/a	n/a
34	POLR2A	chr2:113930884-113933425	GM12892	blood:	n/a	n/a
35	ZNF143	chr2:113931189-113932361	GM12878	blood:	n/a	chr2:113932090-113932109
36	STAT5A	chr2:113930909-113933387	GM12878	blood:	n/a	chr2:113932662-113932674 chr2:113933096-113933104 chr2:113932728-113932740 chr2:113932396-113932408 chr2:113931734-113931746 chr2:113931801-113931813
37	CTCF	chr2:113931080-113931230	GM12875	blood:	n/a	n/a
38	PAX5	chr2:113931202-113931872	GM12878	blood:	n/a	n/a
39	POLR2A	chr2:113931079-113933331	GM12891	blood:	n/a	n/a
40	SPI1	chr2:113931091-113931718	GM12878	blood:	n/a	n/a
41	POLR2A	chr2:113931153-113931996	NB4	blood:	n/a	n/a
42	CTCF	chr2:113931080-113931230	GM12871	blood:	n/a	n/a
43	MAX	chr2:113931066-113931921	GM12878	blood:	n/a	chr2:113931713-113931723
44	CTCF	chr2:113931160-113931310	GM12873	blood:	n/a	n/a
45	RFX5	chr2:113930999-113931646	GM12878	blood:	n/a	n/a
46	POLR2A	chr2:113931222-113931816	K562	blood:	n/a	n/a
47	ZC3H11A	chr2:113931190-113931635	K562	blood:	n/a	n/a
48	GABPA	chr2:113931090-113931834	K562	blood:	n/a	n/a
49	ZBTB7A	chr2:113931105-113931579	K562	blood:	n/a	n/a
50	PAX5	chr2:113931095-113931699	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113930203..113932925-chr2:113950004..113952772,2	K562	blood:
2	chr2:113919676..113922508-chr2:113929408..113931402,2	K562	blood:
3	chr2:113913340..113916449-chr2:113931202..113934969,5	MCF-7	breast:
4	chr2:113913826..113916797-chr2:113930139..113933348,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAX8-1	chr2:113931180-113931671	ENSG00000234174.1

Variant related genes	Relation type
PSD4	TF binding region
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs45492502	1.00[AFR][1000 genomes]
rs45545633	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113916000-113939000	Weak transcription	Right Atrium	heart
2	chr2:113923000-113932200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:113923000-113951800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:113923000-113956000	Weak transcription	HMEC	breast
5	chr2:113923200-113931600	Weak transcription	Brain Anterior Caudate	brain
6	chr2:113923800-113931400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:113923800-113937800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:113926600-113932600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:113926800-113931600	Weak transcription	Esophagus	oesophagus
10	chr2:113927600-113936200	Weak transcription	NHEK	skin
11	chr2:113928000-113935800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:113928600-113931600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:113929600-113932800	Enhancers	Stomach Mucosa	stomach
14	chr2:113930000-113931400	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr2:113930200-113931400	Enhancers	Liver	Liver
16	chr2:113930200-113931600	Enhancers	Colonic Mucosa	Colon
17	chr2:113930200-113931600	Enhancers	Placenta	Placenta
18	chr2:113930200-113931600	Enhancers	Gastric	stomach
19	chr2:113930200-113931600	Enhancers	Lung	lung
20	chr2:113930200-113935200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:113930400-113931400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr2:113930400-113934200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr2:113930600-113931400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr2:113930600-113931400	Flanking Active TSS	Dnd41	blood
25	chr2:113930600-113931600	Weak transcription	Fetal Intestine Small	intestine
26	chr2:113930600-113931600	Weak transcription	Small Intestine	intestine
27	chr2:113930600-113934200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:113930600-113934600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr2:113930800-113931400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr2:113930800-113931400	Flanking Active TSS	GM12878-XiMat	blood
31	chr2:113930800-113931600	Flanking Active TSS	Primary B cells from peripheral blood	blood
32	chr2:113930800-113931600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr2:113930800-113931600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr2:113930800-113931600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:113930800-113931600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:113930800-113934000	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr2:113930800-113937800	Weak transcription	Pancreas	Pancrea
38	chr2:113931000-113931400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:113931000-113931400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr2:113931000-113931400	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr2:113931000-113931400	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr2:113931000-113931400	Flanking Active TSS	K562	blood
43	chr2:113931000-113931600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr2:113931000-113931600	Weak transcription	Spleen	Spleen
45	chr2:113931000-113931800	Flanking Active TSS	HepG2	liver
46	chr2:113931000-113933600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr2:113931000-113933800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:113931000-113934000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:113931000-113934200	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr2:113931000-113934200	Active TSS	Rectal Smooth Muscle	rectum

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