Variant report

Variant	rs744661
Chromosome Location	chr3:111852761-111852762
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	NFATC1	chr3:111846287-111853296	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:111850784-111853964	GM12891	blood:	n/a	n/a
3	RUNX3	chr3:111850883-111854136	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:111846191-111854054	GM12892	blood:	n/a	n/a
5	POU2F2	chr3:111852468-111853376	GM12878	blood:	n/a	n/a
6	EBF1	chr3:111851012-111856368	GM12878	blood:	n/a	chr3:111852245-111852256
7	RUNX3	chr3:111850936-111853979	GM12878	blood:	n/a	n/a
8	EP300	chr3:111851070-111854042	GM12878	blood:	n/a	chr3:111851867-111851881 chr3:111851873-111851887 chr3:111852008-111852017
9	PML	chr3:111850554-111854266	GM12878	blood:	n/a	chr3:111852106-111852114
10	STAT5A	chr3:111850377-111854015	GM12878	blood:	n/a	chr3:111851865-111851876 chr3:111851072-111851092 chr3:111851295-111851306
11	E2F4	chr3:111851768-111852781	GM12878	blood:	n/a	n/a
12	EBF1	chr3:111852523-111853268	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:111852490-111852941	GM12891	blood:	n/a	n/a
14	RELA	chr3:111851497-111852862	GM10847	blood:	n/a	n/a
15	POLR2A	chr3:111850789-111854058	GM12892	blood:	n/a	n/a
16	POLR2A	chr3:111850717-111854239	GM12892	blood:	n/a	n/a
17	TBP	chr3:111848676-111853001	GM12878	blood:	n/a	n/a
18	BCLAF1	chr3:111850867-111854010	GM12878	blood:	n/a	chr3:111851873-111851882 chr3:111852251-111852260 chr3:111851984-111851993 chr3:111852131-111852144
19	CEBPB	chr3:111850869-111852835	GM12878	blood:	n/a	n/a
20	FOXM1	chr3:111850668-111852993	GM12878	blood:	n/a	n/a
21	RELA	chr3:111851431-111853146	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:111850956-111853341	GM19099	blood:	n/a	n/a
23	TBL1XR1	chr3:111850671-111854123	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:111850835-111853668	GM12878	blood:	n/a	n/a
25	RFX5	chr3:111851827-111852821	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:111846299-111854337	Raji	blood:	n/a	n/a
27	NFATC1	chr3:111846108-111854042	GM12878	blood:	n/a	n/a
28	ATF2	chr3:111850797-111852839	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:111852558-111853423	GM12878	blood:	n/a	n/a
30	NFIC	chr3:111849961-111852875	GM12878	blood:	n/a	n/a
31	BCL3	chr3:111851684-111852806	GM12878	blood:	n/a	chr3:111851873-111851882 chr3:111852251-111852260 chr3:111851984-111851993 chr3:111852131-111852144
32	RELA	chr3:111850997-111852870	GM12891	blood:	n/a	n/a
33	NFIC	chr3:111845900-111853068	GM12878	blood:	n/a	n/a
34	CHD2	chr3:111850980-111854030	GM12878	blood:	n/a	n/a
35	WRNIP1	chr3:111852545-111853475	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:111850847-111853999	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:111846063-111856284	GM12878	blood:	n/a	n/a
38	RELA	chr3:111850963-111852972	GM15510	blood:	n/a	n/a
39	POLR2A	chr3:111850803-111853468	GM12891	blood:	n/a	n/a
40	FOXM1	chr3:111850792-111853336	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:111852496-111853708	GM12891	blood:	n/a	n/a
42	USF2	chr3:111851086-111853141	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:111850773-111856379	GM12878	blood:	n/a	n/a
44	POLR2A	chr3:111846207-111853952	GM12892	blood:	n/a	n/a
45	EBF1	chr3:111852537-111852884	GM12878	blood:	n/a	n/a
46	POLR2A	chr3:111852611-111853419	GM12878	blood:	n/a	n/a
47	BCLAF1	chr3:111850777-111854285	GM12878	blood:	n/a	chr3:111851873-111851882 chr3:111852251-111852260 chr3:111851984-111851993 chr3:111852131-111852144
48	POLR2A	chr3:111846124-111855250	GM12878	blood:	n/a	n/a
49	CUX1	chr3:111848565-111852995	GM12878	blood:	n/a	n/a
50	PML	chr3:111850935-111852959	GM12878	blood:	n/a	chr3:111852106-111852114

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf52-1	chr3:111852270-111854206	ENSG00000261488.1

Variant related genes	Relation type
GCSAM	TF binding region

rs_ID	r²[population]
rs1492489	0.81[LWK][hapmap]
rs340170	0.84[ASW][hapmap]

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111812200-111853000	Weak transcription	Right Ventricle	heart
2	chr3:111830600-111853200	Weak transcription	Lung	lung
3	chr3:111834200-111853800	Weak transcription	Fetal Intestine Small	intestine
4	chr3:111839000-111853000	Weak transcription	Left Ventricle	heart
5	chr3:111840800-111855800	Weak transcription	NH-A	brain
6	chr3:111844800-111855800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:111845600-111852800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:111845600-111855800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:111845800-111853200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:111846800-111853000	Weak transcription	Adipose Nuclei	Adipose
11	chr3:111847000-111853200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:111848000-111853200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:111848200-111857000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:111848400-111853800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:111848400-111854600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:111848400-111854800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:111848400-111855800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:111848400-111856000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:111848400-111856800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:111848800-111853600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:111848800-111854200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:111849000-111854800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:111849200-111853000	Weak transcription	Hela-S3	cervix
24	chr3:111849200-111855000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:111849800-111852800	Weak transcription	Pancreas	Pancrea
26	chr3:111849800-111853000	Weak transcription	Small Intestine	intestine
27	chr3:111849800-111853200	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr3:111849800-111853200	Weak transcription	Fetal Heart	heart
29	chr3:111851000-111852800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr3:111851000-111852800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr3:111851000-111853000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr3:111851600-111854600	Enhancers	Primary hematopoietic stem cells	blood
33	chr3:111851800-111853400	Enhancers	Fetal Muscle Leg	muscle
34	chr3:111852000-111853000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:111852000-111853400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:111852000-111853400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:111852000-111853600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr3:111852200-111852800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr3:111852200-111853000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:111852200-111853200	Weak transcription	Stomach Mucosa	stomach
41	chr3:111852200-111853600	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr3:111852200-111854200	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr3:111852200-111855000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr3:111852200-111855200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:111852200-111857000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:111852200-111857600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:111852200-111863400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:111852400-111852800	Weak transcription	Spleen	Spleen
49	chr3:111852400-111853000	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr3:111852400-111853200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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