Variant report

Variant	rs3765801
Chromosome Location	chr1:241695350-241695351
allele	A/C
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	ZNF384	chr1:241694556-241695775	GM12878	blood:	n/a	n/a
2	FOXM1	chr1:241694491-241695579	GM12878	blood:	n/a	n/a
3	ARID3A	chr1:241694493-241695661	HepG2	liver:	n/a	n/a
4	CREB1	chr1:241694609-241695636	GM12878	blood:	n/a	n/a
5	RAD21	chr1:241694558-241695748	GM12878	blood:	n/a	chr1:241694772-241694791
6	ZNF143	chr1:241694587-241695647	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:241695118-241695869	GM12892	blood:	n/a	n/a
8	TBL1XR1	chr1:241694642-241696520	GM12878	blood:	n/a	n/a
9	TAF1	chr1:241695144-241695825	GM12878	blood:	n/a	n/a
10	CTCF	chr1:241694558-241695536	GM12878	blood:	n/a	chr1:241694772-241694788 chr1:241694771-241694789 chr1:241694773-241694794 chr1:241695045-241695054
11	IRF1	chr1:241694611-241695765	K562	blood:	n/a	chr1:241695377-241695391 chr1:241695377-241695394 chr1:241695376-241695389 chr1:241695379-241695390 chr1:241695380-241695390 chr1:241695376-241695389 chr1:241695375-241695389 chr1:241695378-241695392 chr1:241695376-241695390 chr1:241694857-241694866 chr1:241695378-241695389 chr1:241695377-241695391 chr1:241695377-241695390 chr1:241695376-241695389 chr1:241695370-241695390 chr1:241695374-241695388
12	SPI1	chr1:241694594-241695401	HL-60	blood:	n/a	chr1:241694854-241694863 chr1:241694852-241694865
13	RUNX3	chr1:241694636-241695816	GM12878	blood:	n/a	chr1:241695259-241695268 chr1:241695259-241695268
14	POLR2A	chr1:241694748-241695400	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr1:241694524-241695874	GM12891	blood:	n/a	n/a
16	BHLHE40	chr1:241694463-241695736	GM12878	blood:	n/a	n/a
17	TBL1XR1	chr1:241694589-241695753	K562	blood:	n/a	n/a
18	NFIC	chr1:241694622-241695774	GM12878	blood:	n/a	n/a
19	RAD21	chr1:241694559-241695422	Hela-S3	cervix:	n/a	chr1:241694772-241694791
20	MEF2A	chr1:241694623-241695629	GM12878	blood:	n/a	n/a
21	RUNX3	chr1:241694524-241695818	GM12878	blood:	n/a	chr1:241695259-241695268 chr1:241695259-241695268
22	MAZ	chr1:241694597-241695756	K562	blood:	n/a	n/a
23	MEF2C	chr1:241694659-241695730	GM12878	blood:	n/a	n/a
24	GTF3C2	chr1:241694590-241695598	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr1:241694086-241695371	SK-N-SH	brain:	n/a	chr1:241694772-241694788 chr1:241694771-241694789 chr1:241694773-241694794 chr1:241695045-241695054
26	BCLAF1	chr1:241694508-241695854	GM12878	blood:	n/a	chr1:241694855-241694864
27	EBF1	chr1:241694619-241695540	GM12878	blood:	n/a	n/a
28	REST	chr1:241694698-241695368	HL-60	blood:	n/a	n/a
29	ZNF384	chr1:241694504-241695576	K562	blood:	n/a	n/a
30	IRF1	chr1:241694628-241695817	K562	blood:	n/a	chr1:241695377-241695391 chr1:241695377-241695394 chr1:241695376-241695389 chr1:241695379-241695390 chr1:241695380-241695390 chr1:241695376-241695389 chr1:241695375-241695389 chr1:241695378-241695392 chr1:241695376-241695390 chr1:241694857-241694866 chr1:241695378-241695389 chr1:241695377-241695391 chr1:241695377-241695390 chr1:241695376-241695389 chr1:241695370-241695390 chr1:241695374-241695388
31	MEF2A	chr1:241694543-241695672	GM12878	blood:	n/a	n/a
32	ATF2	chr1:241694596-241695663	GM12878	blood:	n/a	n/a
33	ARID3A	chr1:241694536-241695353	K562	blood:	n/a	n/a
34	SMC3	chr1:241694184-241695696	GM12878	blood:	n/a	chr1:241694773-241694787
35	RFX5	chr1:241694716-241695380	K562	blood:	n/a	n/a
36	MAFF	chr1:241694669-241695362	K562	blood:	n/a	n/a
37	RAD21	chr1:241694400-241695365	SK-N-SH	brain:	n/a	chr1:241694772-241694791
38	CTCF	chr1:241694269-241695639	A549	lung:	n/a	chr1:241694772-241694788 chr1:241694771-241694789 chr1:241694773-241694794 chr1:241695045-241695054
39	MTA3	chr1:241694504-241695885	GM12878	blood:	n/a	n/a
40	EP300	chr1:241694568-241695392	K562	blood:	n/a	chr1:241694853-241694867 chr1:241694854-241694863
41	CEBPB	chr1:241694593-241695366	Hela-S3	cervix:	n/a	chr1:241694895-241694908
42	POLR2A	chr1:241695194-241695748	MCF10A-Er-Src	breast:	n/a	n/a
43	CUX1	chr1:241694536-241695509	GM12878	blood:	n/a	chr1:241694579-241694595
44	FOXM1	chr1:241694623-241695797	GM12878	blood:	n/a	n/a
45	EP300	chr1:241694689-241695823	GM12878	blood:	n/a	chr1:241695409-241695423 chr1:241694853-241694867 chr1:241695379-241695393 chr1:241694854-241694863
46	CTCF	chr1:241695280-241695430	HUVEC	blood vessel:	n/a	n/a
47	CTCF	chr1:241694448-241695479	HCT-116	colon:	n/a	chr1:241694772-241694788 chr1:241694771-241694789 chr1:241694773-241694794 chr1:241695045-241695054
48	MYC	chr1:241694594-241695769	NB4	blood:	n/a	n/a
49	SPI1	chr1:241694495-241695376	GM12878	blood:	n/a	chr1:241694854-241694863 chr1:241694852-241694865
50	JUND	chr1:241694591-241695712	K562	blood:	n/a	chr1:241695616-241695627

No.	Distal block	Cell Line	Cell type
1	chr1:241693526..241696085-chr1:241801417..241805051,3	MCF-7	breast:
2	chr1:241692902..241697485-chr1:242010276..242014432,6	K562	blood:
3	chr1:241693547..241697485-chr1:242010276..242012986,4	K562	blood:

Variant related genes	Relation type
KMO	TF binding region
ENSG00000054277	Chromatin interaction
ENSG00000174371	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10802967	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10926503	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10926511	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12059383	0.85[YRI][hapmap]
rs12062672	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12065955	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12072983	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2105079	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341939	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4660098	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4660102	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57644653	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540071	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv949442	chr1:241432051-241730054	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv873371	chr1:241667244-241747838	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241694400-241695600	Active TSS	Brain Anterior Caudate	brain
2	chr1:241694400-241695600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:241694400-241696600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr1:241694600-241695400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr1:241694600-241695400	Flanking Active TSS	Hela-S3	cervix
6	chr1:241694600-241695600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:241694600-241695600	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr1:241694600-241695600	Active TSS	Muscle Satellite Cultured Cells	--
9	chr1:241694600-241695600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:241694600-241695600	Active TSS	Brain Cingulate Gyrus	brain
11	chr1:241694600-241695600	Active TSS	Brain Hippocampus Middle	brain
12	chr1:241694600-241695600	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr1:241694600-241695600	Active TSS	Thymus	Thymus
14	chr1:241694600-241695600	Active TSS	HepG2	liver
15	chr1:241694600-241695600	Active TSS	HMEC	breast
16	chr1:241694600-241695600	Flanking Active TSS	HUVEC	blood vessel
17	chr1:241694600-241695600	Active TSS	NHLF	lung
18	chr1:241694600-241695800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr1:241694600-241695800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:241694600-241695800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:241694600-241695800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:241694600-241695800	Active TSS	Brain Angular Gyrus	brain
23	chr1:241694600-241695800	Active TSS	Colonic Mucosa	Colon
24	chr1:241694600-241695800	Active TSS	Colon Smooth Muscle	Colon
25	chr1:241694600-241695800	Active TSS	Fetal Brain Male	brain
26	chr1:241694600-241695800	Active TSS	Fetal Intestine Small	intestine
27	chr1:241694600-241695800	Active TSS	Fetal Thymus	thymus
28	chr1:241694600-241695800	Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr1:241694600-241696000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:241694600-241696200	Active TSS	Liver	Liver
31	chr1:241694600-241696200	Active TSS	GM12878-XiMat	blood
32	chr1:241694600-241696400	Active TSS	Brain Substantia Nigra	brain
33	chr1:241694600-241697000	Active TSS	Duodenum Mucosa	Duodenum
34	chr1:241694600-241697200	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr1:241694800-241695400	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr1:241694800-241695400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:241694800-241695400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:241694800-241695400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:241694800-241695400	Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr1:241694800-241695400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:241694800-241695400	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr1:241694800-241695400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr1:241694800-241695400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:241694800-241695400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:241694800-241695400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr1:241694800-241695400	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr1:241694800-241695400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:241694800-241695400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:241694800-241695400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:241694800-241695400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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