Variant report

Variant	rs9724980
Chromosome Location	chr1:246023204-246023205
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	EP300	chr1:246022955-246023357	SK-N-SH_RA	brain:	n/a	chr1:246022993-246023006 chr1:246023251-246023258
2	MAX	chr1:246022996-246023547	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr1:246021182-246023742	SK-N-SH	brain:	n/a	chr1:246023449-246023461 chr1:246022486-246022505 chr1:246023128-246023140
4	TCF12	chr1:246022303-246025049	SK-N-SH	brain:	n/a	chr1:246023295-246023302
5	GATA3	chr1:246022173-246024985	SK-N-SH	brain:	n/a	chr1:246023944-246023954
6	STAT3	chr1:246023095-246023356	MCF10A-Er-Src	breast:	n/a	chr1:246023206-246023215 chr1:246023169-246023176
7	PBX3	chr1:246022865-246023473	SK-N-SH	brain:	n/a	n/a
8	FOS	chr1:246022617-246023450	MCF10A-Er-Src	breast:	n/a	chr1:246023207-246023214 chr1:246022736-246022748 chr1:246022738-246022746 chr1:246022734-246022745 chr1:246023226-246023237 chr1:246023205-246023216
9	POLR2A	chr1:246022937-246023792	SK-N-SH	brain:	n/a	n/a
10	FOS	chr1:246022543-246023410	HUVEC	blood vessel:	n/a	chr1:246023207-246023214 chr1:246022736-246022748 chr1:246022738-246022746 chr1:246022734-246022745 chr1:246023226-246023237 chr1:246023205-246023216
11	MYC	chr1:246023138-246023451	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr1:246023043-246023388	MCF10A-Er-Src	breast:	n/a	chr1:246023207-246023214 chr1:246023226-246023237 chr1:246023205-246023216
13	STAT3	chr1:246023068-246023387	MCF10A-Er-Src	breast:	n/a	chr1:246023206-246023215 chr1:246023169-246023176
14	GATA3	chr1:246022488-246023531	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr1:246022367-246023477	K562	blood:	n/a	n/a
16	CTCF	chr1:246021299-246023512	SK-N-SH	brain:	n/a	chr1:246022489-246022496 chr1:246022487-246022508
17	STAT3	chr1:246023056-246023343	MCF10A-Er-Src	breast:	n/a	chr1:246023206-246023215 chr1:246023169-246023176
18	POLR2A	chr1:246022980-246023388	U87	brain:	n/a	n/a
19	GATA1	chr1:246022536-246023380	PBDE	blood:	n/a	n/a
20	POLR2A	chr1:246019287-246025503	K562	blood:	n/a	n/a
21	POLR2A	chr1:246022779-246023470	U87	brain:	n/a	n/a
22	PBX3	chr1:246022507-246023528	SK-N-SH	brain:	n/a	n/a
23	CEBPB	chr1:246023105-246023364	IMR90	lung:	n/a	n/a
24	FOS	chr1:246023023-246023451	MCF10A-Er-Src	breast:	n/a	chr1:246023207-246023214 chr1:246023226-246023237 chr1:246023205-246023216
25	POLR2A	chr1:246022169-246024641	IMR90	lung:	n/a	n/a
26	STAT3	chr1:246023125-246023385	MCF10A-Er-Src	breast:	n/a	chr1:246023206-246023215 chr1:246023169-246023176
27	E2F4	chr1:246023104-246023322	MCF10A-Er-Src	breast:	n/a	n/a
28	GATA2	chr1:246022735-246023350	HUVEC	blood vessel:	n/a	n/a
29	EP300	chr1:246023019-246023339	SK-N-SH_RA	brain:	n/a	chr1:246023251-246023258
30	FOS	chr1:246023021-246023412	MCF10A-Er-Src	breast:	n/a	chr1:246023207-246023214 chr1:246023226-246023237 chr1:246023205-246023216
31	RAD21	chr1:246023095-246023430	IMR90	lung:	n/a	chr1:246023128-246023140
32	MYC	chr1:246023160-246023385	MCF10A-Er-Src	breast:	n/a	n/a
33	FOSL2	chr1:246022426-246023449	SK-N-SH	brain:	n/a	chr1:246023207-246023214 chr1:246022736-246022748 chr1:246022738-246022746 chr1:246022734-246022745

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246015163..246018101-chr1:246022142..246024393,2	K562	blood:
2	chr1:246019584..246021288-chr1:246022955..246025126,2	MCF-7	breast:

Variant related genes	Relation type
SMYD3	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10737776	1.00[YRI][hapmap]
rs10754478	1.00[YRI][hapmap]
rs10754482	1.00[YRI][hapmap]
rs10924344	1.00[YRI][hapmap]
rs4233245	1.00[YRI][hapmap]
rs4314852	1.00[YRI][hapmap]
rs4314853	1.00[YRI][hapmap]
rs4451526	1.00[YRI][hapmap]
rs4654165	1.00[YRI][hapmap]
rs9287191	1.00[YRI][hapmap]
rs9287199	1.00[YRI][hapmap]
rs9287201	1.00[YRI][hapmap]
rs9727572	1.00[YRI][hapmap]
rs9727618	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007728	chr1:245235174-246156455	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv497871	chr1:245706209-246655353	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv534412	chr1:245747724-246655416	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1003594	chr1:245801793-246649329	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1004412	chr1:245830921-246169054	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv535385	chr1:245830921-246169054	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1011255	chr1:245913512-246065050	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv998801	chr1:245924108-246131115	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv535386	chr1:245924108-246131115	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1014841	chr1:245936464-246143222	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv535387	chr1:245936464-246143222	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1008786	chr1:245948622-246514454	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv535388	chr1:245948622-246514454	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv468805	chr1:245950642-246229245	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv549521	chr1:245950642-246229245	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv1004119	chr1:245957145-246813150	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	nsv535389	chr1:245957145-246813150	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	nsv1014529	chr1:245957145-246817877	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
19	nsv873405	chr1:245959911-246093644	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv1000654	chr1:245966390-246778182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
21	nsv535392	chr1:245966390-246778182	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
22	nsv868852	chr1:245969229-246811220	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
23	nsv873406	chr1:245991027-246039231	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	nsv1005074	chr1:245999762-246141613	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	nsv1013699	chr1:246005308-246143361	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
26	nsv535393	chr1:246005308-246143361	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:245991000-246045000	Weak transcription	Spleen	Spleen
2	chr1:245997600-246023800	Weak transcription	Ovary	ovary
3	chr1:245999400-246024200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:245999800-246038400	Weak transcription	Aorta	Aorta
5	chr1:246001200-246023400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:246001800-246056800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:246006800-246041200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:246009600-246038200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:246010200-246028200	Weak transcription	Thymus	Thymus
10	chr1:246012000-246024800	Weak transcription	Esophagus	oesophagus
11	chr1:246012800-246049600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:246014200-246026400	Weak transcription	Brain Anterior Caudate	brain
13	chr1:246015200-246028000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:246015400-246038200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:246016000-246024800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:246017800-246036400	Weak transcription	Right Ventricle	heart
17	chr1:246018000-246026000	Weak transcription	Primary B cells from cord blood	blood
18	chr1:246018200-246026800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:246018400-246026000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:246019000-246025200	Enhancers	NH-A	brain
21	chr1:246019200-246025200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:246019200-246067400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:246019400-246024600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:246020200-246028800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:246020200-246036000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:246020400-246023800	Weak transcription	Fetal Brain Female	brain
27	chr1:246020600-246023400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:246020600-246024400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:246020800-246023400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:246021000-246023800	Weak transcription	HSMMtube	muscle
31	chr1:246021000-246027200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:246021000-246038200	Weak transcription	Pancreas	Pancrea
33	chr1:246021200-246025400	Enhancers	NHLF	lung
34	chr1:246021400-246026200	Weak transcription	HepG2	liver
35	chr1:246021400-246029400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:246021600-246025000	Enhancers	Fetal Stomach	stomach
37	chr1:246021800-246025400	Enhancers	NHDF-Ad	bronchial
38	chr1:246022000-246026000	Weak transcription	Primary T cells from cord blood	blood
39	chr1:246022000-246026600	Weak transcription	Dnd41	blood
40	chr1:246022000-246028800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:246022000-246037800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:246022000-246038200	Weak transcription	Gastric	stomach
43	chr1:246022000-246042600	Weak transcription	Fetal Intestine Small	intestine
44	chr1:246022200-246037800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:246022400-246023600	Enhancers	Placenta	Placenta
46	chr1:246022400-246024200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:246022400-246024800	Enhancers	Muscle Satellite Cultured Cells	--
48	chr1:246022600-246023400	Enhancers	HUVEC	blood vessel
49	chr1:246022600-246023600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:246022600-246023600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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