Variant report

Variant	rs376001449
Chromosome Location	chr1:226249160-226249161
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	POLR2A	chr1:226249047-226251609	Hela-S3	cervix:	n/a	n/a
2	CHD1	chr1:226248795-226252344	IMR90	lung:	n/a	chr1:226250205-226250215 chr1:226250686-226250696 chr1:226250156-226250166 chr1:226250759-226250769 chr1:226250029-226250039
3	CREB1	chr1:226249067-226250858	K562	blood:	n/a	n/a
4	MXI1	chr1:226248834-226251514	Hela-S3	cervix:	n/a	n/a
5	YY1	chr1:226249133-226251486	SK-N-SH	brain:	n/a	chr1:226249735-226249749 chr1:226249769-226249780 chr1:226250437-226250446 chr1:226250796-226250807 chr1:226250432-226250446 chr1:226250678-226250692 chr1:226249556-226249575 chr1:226249558-226249580 chr1:226250013-226250022 chr1:226249561-226249569 chr1:226250412-226250420 chr1:226250442-226250451 chr1:226250678-226250687 chr1:226250799-226250808 chr1:226250972-226250984
6	BCLAF1	chr1:226249142-226250288	K562	blood:	n/a	chr1:226249777-226249790 chr1:226249655-226249668 chr1:226249771-226249784 chr1:226249778-226249791 chr1:226250007-226250016
7	PML	chr1:226249030-226251155	K562	blood:	n/a	n/a
8	POLR2A	chr1:226249112-226251663	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr1:226248810-226256763	K562	blood:	n/a	n/a
10	NFIC	chr1:226249138-226249953	HepG2	liver:	n/a	n/a
11	MTA3	chr1:226249141-226249704	GM12878	blood:	n/a	n/a
12	SMC3	chr1:226249106-226250838	Hela-S3	cervix:	n/a	chr1:226250669-226250683 chr1:226249498-226249505
13	POLR2A	chr1:226249126-226251671	K562	blood:	n/a	n/a
14	POLR2A	chr1:226249055-226251570	K562	blood:	n/a	n/a
15	MAFK	chr1:226249020-226249909	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:226249009-226251573	HL-60	blood:	n/a	n/a
17	MAX	chr1:226249072-226250569	A549	lung:	n/a	n/a
18	SIN3A	chr1:226249154-226252868	H1-hESC	embryonic stem cell:	n/a	chr1:226250460-226250473 chr1:226249897-226249908
19	BACH1	chr1:226248969-226249540	K562	blood:	n/a	n/a
20	UBTF	chr1:226249095-226252188	K562	blood:	n/a	n/a
21	MXI1	chr1:226248469-226253081	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr1:226248825-226250749	K562	blood:	n/a	n/a
23	POLR2A	chr1:226248930-226251683	PANC-1	pancreas:	n/a	n/a
24	TBP	chr1:226248936-226249887	Hela-S3	cervix:	n/a	n/a
25	PML	chr1:226249130-226250274	GM12878	blood:	n/a	n/a
26	MAX	chr1:226249160-226251587	ECC-1	luminal epithelium:	n/a	chr1:226251147-226251156 chr1:226251147-226251156 chr1:226251146-226251157 chr1:226251148-226251155
27	POLR2A	chr1:226248882-226252317	Hela-S3	cervix:	n/a	n/a
28	MAX	chr1:226249043-226251559	SK-N-SH	brain:	n/a	chr1:226251147-226251156 chr1:226251147-226251156 chr1:226251146-226251157 chr1:226251148-226251155
29	POLR2A	chr1:226248825-226251497	HepG2	liver:	n/a	n/a
30	GTF2F1	chr1:226249071-226249535	Hela-S3	cervix:	n/a	n/a
31	STAT5A	chr1:226248846-226250015	K562	blood:	n/a	chr1:226249037-226249060
32	GTF2F1	chr1:226249132-226249956	K562	blood:	n/a	n/a
33	EP300	chr1:226248727-226250570	K562	blood:	n/a	chr1:226249804-226249813 chr1:226250435-226250444 chr1:226249779-226249795 chr1:226250165-226250174 chr1:226249473-226249489
34	ZNF274	chr1:226248726-226249791	K562	blood:	n/a	n/a
35	TAL1	chr1:226249048-226249933	K562	blood:	n/a	n/a
36	POLR2A	chr1:226249100-226250200	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr1:226249148-226251616	HUVEC	blood vessel:	n/a	n/a
38	CTCF	chr1:226249160-226249310	HRE	kidney:	n/a	n/a
39	POLR2A	chr1:226249059-226251040	HL-60	blood:	n/a	n/a
40	GATA3	chr1:226248722-226249322	SH-SY5Y	brain:	n/a	n/a
41	TEAD4	chr1:226248646-226250254	K562	blood:	n/a	n/a
42	BRCA1	chr1:226249081-226249274	H1-hESC	embryonic stem cell:	n/a	n/a
43	MYC	chr1:226248852-226251406	A549	lung:	n/a	chr1:226251147-226251156 chr1:226251147-226251156 chr1:226251146-226251157 chr1:226251148-226251155
44	RFX5	chr1:226248840-226250583	Hela-S3	cervix:	n/a	chr1:226250349-226250358 chr1:226249252-226249261
45	POLR2A	chr1:226248773-226252207	MCF10A-Er-Src	breast:	n/a	n/a
46	IRF1	chr1:226248569-226249959	K562	blood:	n/a	chr1:226248768-226248785 chr1:226248945-226248959
47	POLR2A	chr1:226249100-226251609	K562	blood:	n/a	n/a
48	RCOR1	chr1:226248891-226250820	K562	blood:	n/a	n/a
49	ELK1	chr1:226249156-226249843	K562	blood:	n/a	n/a
50	MYC	chr1:226248836-226252204	K562	blood:	n/a	chr1:226251147-226251156 chr1:226251147-226251156 chr1:226251146-226251157 chr1:226251148-226251155

No.	Distal block	Cell Line	Cell type
1	chr1:226053730..226055639-chr1:226248303..226251048,2	MCF-7	breast:
2	chr1:226183087..226192322-chr1:226243551..226254243,95	K562	blood:
3	chr1:226247680..226258196-chr1:226306136..226315725,36	MCF-7	breast:
4	chr1:225964211..225968767-chr1:226248453..226252378,4	K562	blood:
5	chr1:226183029..226192481-chr1:226247725..226253108,31	MCF-7	breast:
6	chr1:226184876..226191468-chr1:226247585..226254254,12	MCF-7	breast:
7	chr1:226249145..226251355-chr5:138634621..138637026,2	MCF-7	breast:
8	chr1:144533790..144534425-chr1:226249029..226249552,2	Hela-S3	cervix:
9	chr1:226248937..226249745-chr3:135914572..135915298,2	Hela-S3	cervix:
10	chr1:226247090..226249451-chr1:226292552..226294249,2	K562	blood:
11	chr1:225838732..225840997-chr1:226248323..226251215,2	MCF-7	breast:
12	chr1:226248851..226254336-chr1:226269112..226274282,12	MCF-7	breast:
13	chr1:226248789..226253333-chr1:226269675..226273948,8	MCF-7	breast:
14	chr1:225964614..225966521-chr1:226248789..226250672,2	K562	blood:
15	chr1:226247784..226253760-chr1:226305545..226317702,29	MCF-7	breast:
16	chr1:226178791..226193771-chr1:226246813..226256535,111	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf55-1	chr1:226245769-226249546	NONHSAT009869

Variant related genes	Relation type
H3F3A	TF binding region
ENSG00000154380	Chromatin interaction
ENSG00000174579	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000196187	Chromatin interaction
ENSG00000225518	Chromatin interaction
ENSG00000199545	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000270598	Chromatin interaction
ENSG00000201699	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription 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	68 gene(s)	inside rSNPs	diseases
3	esv3327023	chr1:226248854-226251702	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226229800-226249400	Weak transcription	Spleen	Spleen
2	chr1:226230000-226249200	Weak transcription	Aorta	Aorta
3	chr1:226231200-226249200	Weak transcription	Pancreas	Pancrea
4	chr1:226232000-226249200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:226232200-226249400	Weak transcription	Gastric	stomach
6	chr1:226235200-226249200	Weak transcription	Small Intestine	intestine
7	chr1:226235400-226249200	Weak transcription	Esophagus	oesophagus
8	chr1:226241000-226249200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:226242400-226249200	Weak transcription	Lung	lung
10	chr1:226242800-226249200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:226244000-226249400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:226247600-226249200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:226248200-226249200	Enhancers	Primary B cells from peripheral blood	blood
14	chr1:226248200-226249200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:226248200-226249200	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr1:226248200-226249200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:226248200-226249400	Flanking Active TSS	Fetal Heart	heart
18	chr1:226248200-226249600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr1:226248200-226249600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:226248200-226249600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr1:226248200-226253400	Active TSS	H9 Cell Line	embryonic stem cell
22	chr1:226248400-226249200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr1:226248600-226249200	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr1:226248600-226249200	Flanking Active TSS	HepG2	liver
25	chr1:226248600-226249400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:226248600-226249400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr1:226248600-226249400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr1:226248600-226249400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr1:226248600-226249400	Flanking Active TSS	Rectal Smooth Muscle	rectum
30	chr1:226248600-226249400	Flanking Active TSS	A549	lung
31	chr1:226248600-226249400	Flanking Active TSS	K562	blood
32	chr1:226248600-226249600	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr1:226248600-226249600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:226248600-226249800	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr1:226248800-226249200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:226248800-226249200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:226248800-226249200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr1:226248800-226249200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:226248800-226249200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:226248800-226249200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:226248800-226249200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:226248800-226249200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:226248800-226249200	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr1:226248800-226249200	Flanking Active TSS	Fetal Intestine Small	intestine
45	chr1:226248800-226249200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr1:226248800-226249400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr1:226248800-226249400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr1:226248800-226249400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr1:226248800-226249400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:226248800-226249400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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