Variant report

Variant	rs2297652
Chromosome Location	chr1:46049571-46049572
allele	C/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	POLR2A	chr1:46049351-46050894	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr1:46048858-46050950	SK-N-MC	brain:	n/a	n/a
3	NRF1	chr1:46048970-46049912	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:46049208-46050909	MCF-7	breast:	n/a	n/a
5	REST	chr1:46049570-46049968	HepG2	liver:	n/a	n/a
6	TAF1	chr1:46049533-46049855	SK-N-SH	brain:	n/a	n/a
7	E2F4	chr1:46048903-46051150	MCF10A-Er-Src	breast:	n/a	chr1:46050291-46050298 chr1:46050291-46050302 chr1:46050442-46050449 chr1:46050438-46050450 chr1:46050291-46050302 chr1:46050290-46050300 chr1:46050288-46050305 chr1:46050441-46050449 chr1:46050292-46050307 chr1:46050439-46050450 chr1:46049589-46049598 chr1:46049963-46049975 chr1:46050442-46050449 chr1:46050290-46050299 chr1:46050422-46050431 chr1:46050117-46050127 chr1:46050291-46050302 chr1:46050288-46050305 chr1:46050292-46050303 chr1:46049849-46049864 chr1:46050294-46050303 chr1:46050442-46050449 chr1:46050290-46050298 chr1:46050295-46050302 chr1:46050187-46050196 chr1:46050293-46050303 chr1:46050097-46050106 chr1:46050077-46050087 chr1:46050441-46050450 chr1:46050291-46050302 chr1:46050288-46050305 chr1:46050291-46050302 chr1:46050290-46050301
8	TAF1	chr1:46049480-46050233	HepG2	liver:	n/a	n/a
9	NFATC1	chr1:46049272-46049984	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:46049512-46049947	A549	lung:	n/a	n/a
11	GABPA	chr1:46049500-46049712	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:46048954-46050883	GM12878	blood:	n/a	n/a
13	CTCF	chr1:46049506-46050350	K562	blood:	n/a	chr1:46050081-46050094
14	ELF1	chr1:46049399-46049855	A549	lung:	n/a	chr1:46049648-46049659
15	MYC	chr1:46049506-46049799	MCF10A-Er-Src	breast:	n/a	n/a
16	YY1	chr1:46049459-46050593	HCT-116	colon:	n/a	chr1:46050108-46050116 chr1:46050083-46050094 chr1:46050184-46050198 chr1:46050105-46050127 chr1:46050120-46050131 chr1:46050105-46050115 chr1:46049719-46049729 chr1:46050106-46050114 chr1:46050104-46050116 chr1:46050416-46050427 chr1:46050419-46050433 chr1:46050422-46050431 chr1:46050102-46050122 chr1:46050350-46050364 chr1:46050504-46050515 chr1:46050103-46050122
17	MXI1	chr1:46048900-46050948	HepG2	liver:	n/a	n/a
18	RFX5	chr1:46048811-46051051	K562	blood:	n/a	chr1:46049218-46049233 chr1:46050714-46050723 chr1:46050711-46050725
19	EGR1	chr1:46049342-46050590	K562	blood:	n/a	chr1:46050422-46050432 chr1:46050353-46050363 chr1:46049650-46049659 chr1:46050347-46050362 chr1:46050417-46050430 chr1:46050348-46050361 chr1:46050386-46050395 chr1:46050352-46050362 chr1:46050187-46050197
20	ELF1	chr1:46049072-46049938	MCF-7	breast:	n/a	chr1:46049648-46049659
21	E2F6	chr1:46049423-46049613	K562	blood:	n/a	chr1:46049589-46049598
22	CTCF	chr1:46049440-46049590	NHDF-neo	bronchial:	n/a	n/a
23	MAX	chr1:46048880-46051051	HepG2	liver:	n/a	chr1:46050353-46050363
24	POLR2A	chr1:46048871-46050673	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr1:46049518-46050137	Gliobla	brain:	n/a	n/a
26	TAF1	chr1:46049506-46049902	GM12891	blood:	n/a	n/a
27	ELF1	chr1:46048865-46049944	K562	blood:	n/a	chr1:46049648-46049659
28	TAF1	chr1:46049069-46050698	K562	blood:	n/a	n/a
29	POLR2A	chr1:46048828-46050692	GM18505	blood:	n/a	n/a
30	POLR2A	chr1:46049436-46050238	HepG2	liver:	n/a	n/a
31	TAF7	chr1:46049453-46050342	H1-hESC	embryonic stem cell:	n/a	n/a
32	IRF1	chr1:46048937-46050685	K562	blood:	n/a	chr1:46050352-46050366 chr1:46050421-46050435 chr1:46049105-46049119 chr1:46050186-46050200 chr1:46049660-46049674
33	STAT5A	chr1:46049058-46050215	GM12878	blood:	n/a	n/a
34	TAF1	chr1:46048951-46050301	ECC-1	luminal epithelium:	n/a	n/a
35	CUX1	chr1:46049400-46050038	K562	blood:	n/a	n/a
36	POLR2A	chr1:46048746-46051005	GM12892	blood:	n/a	n/a
37	POLR2A	chr1:46049519-46049631	A549	lung:	n/a	n/a
38	CHD2	chr1:46048993-46049992	GM12878	blood:	n/a	n/a
39	HMGN3	chr1:46049555-46050657	K562	blood:	n/a	n/a
40	ELF1	chr1:46048929-46050056	GM12878	blood:	n/a	chr1:46049648-46049659
41	TCF7L2	chr1:46048962-46050123	HCT-116	colon:	n/a	n/a
42	SP4	chr1:46049068-46050847	H1-hESC	embryonic stem cell:	n/a	chr1:46050350-46050366 chr1:46049103-46049119 chr1:46050417-46050433 chr1:46049658-46049674 chr1:46050367-46050383 chr1:46050348-46050364 chr1:46050419-46050435 chr1:46049101-46049117
43	TAF1	chr1:46049452-46050636	SK-N-SH	brain:	n/a	n/a
44	BHLHE40	chr1:46048883-46050815	GM12878	blood:	n/a	chr1:46050116-46050132 chr1:46050417-46050433 chr1:46050048-46050064 chr1:46050163-46050179
45	POLR2A	chr1:46049106-46050964	Hela-S3	cervix:	n/a	n/a
46	ZNF143	chr1:46049038-46050135	K562	blood:	n/a	chr1:46049589-46049599 chr1:46049444-46049453 chr1:46049588-46049606
47	NFIC	chr1:46049096-46050015	GM12878	blood:	n/a	n/a
48	CHD2	chr1:46048958-46050857	Hela-S3	cervix:	n/a	n/a
49	IRF4	chr1:46049266-46050018	GM12878	blood:	n/a	n/a
50	POLR2A	chr1:46049504-46050047	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:46012797..46020877-chr1:46047985..46055272,23	K562	blood:
2	chr1:46047808..46051262-chr1:46767344..46769900,3	K562	blood:
3	chr1:46049473..46050092-chr7:98476104..98476798,2	Hela-S3	cervix:
4	chr1:46049279..46050168-chr10:129796124..129796643,2	Hela-S3	cervix:
5	chr1:46048444..46052841-chr10:129795145..129798145,4	K562	blood:
6	chr1:45185636..45188407-chr1:46047872..46052515,5	K562	blood:
7	chr1:45973068..45975148-chr1:46049390..46051110,2	MCF-7	breast:
8	chr1:46048178..46050215-chr1:46089233..46091590,2	K562	blood:
9	chr1:46047578..46050794-chr1:46077080..46080053,4	K562	blood:
10	chr1:45283391..45288738-chr1:46048072..46051277,6	K562	blood:
11	chr1:45963397..45969763-chr1:46047572..46053150,23	K562	blood:
12	chr1:45194369..45197773-chr1:46046767..46051199,5	K562	blood:
13	chr1:46049223..46051857-chr1:46080346..46084237,3	K562	blood:
14	chr1:45986151..45989227-chr1:46047437..46050636,3	MCF-7	breast:
15	chr1:45980210..45995142-chr1:46046095..46057139,89	K562	blood:
16	chr1:45803780..45809046-chr1:46047811..46052394,14	K562	blood:
17	chr1:46014878..46016600-chr1:46048610..46051417,2	MCF-7	breast:
18	chr1:45974971..45980027-chr1:46048272..46053531,9	K562	blood:
19	chr1:46048876..46050473-chr1:46099079..46101619,2	K562	blood:
20	chr1:46049190..46051065-chr1:46268579..46270111,2	K562	blood:
21	chr1:46026984..46033199-chr1:46047562..46051151,12	K562	blood:
22	chr1:45271675..45274360-chr1:46048607..46050864,2	K562	blood:
23	chr1:46048446..46052403-chr1:46150752..46155740,15	K562	blood:
24	chr1:46049211..46052214-chr1:46711116..46714432,3	K562	blood:
25	chr1:46049483..46050216-chr7:155089459..155090029,2	NB4	blood:
26	chr1:46015193..46018509-chr1:46048657..46051369,3	MCF-7	breast:
27	chr1:46049133..46051352-chr1:46267497..46269310,2	MCF-7	breast:
28	chr1:45186130..45188407-chr1:46047872..46051720,5	K562	blood:
29	chr1:46048335..46051372-chr1:46110517..46113642,3	K562	blood:
30	chr1:45477030..45479805-chr1:46047527..46050763,5	K562	blood:
31	chr1:46049506..46051127-chr1:46805584..46807919,2	K562	blood:
32	chr1:46034190..46037574-chr1:46047982..46052662,9	K562	blood:
33	chr1:46048069..46054740-chr1:46150080..46155979,19	K562	blood:
34	chr1:45963437..45971807-chr1:46047572..46053150,22	K562	blood:
35	chr1:46049420..46050202-chr16:2014500..2015413,2	Hela-S3	cervix:
36	chr1:45195288..45198728-chr1:46046767..46051124,6	K562	blood:
37	chr1:46049257..46050103-chr9:19379925..19380868,2	NB4	blood:
38	chr1:45951915..45956979-chr1:46048471..46052743,8	K562	blood:
39	chr1:46049433..46050097-chr16:85060654..85061505,2	Hela-S3	cervix:
40	chr1:46049350..46050132-chr10:129796144..129796644,2	HCT-116	colon:
41	chr1:46049429..46050217-chr11:61583125..61583729,2	Hela-S3	cervix:
42	chr1:45271934..45274901-chr1:46048607..46050252,3	K562	blood:
43	chr1:11968732..11970324-chr1:46049073..46051914,2	K562	blood:
44	chr1:46012228..46018632-chr1:46046407..46053601,17	K562	blood:
45	chr1:45974558..45995867-chr1:46046173..46057010,94	K562	blood:
46	chr1:45284255..45286941-chr1:46048411..46051884,4	K562	blood:
47	chr1:46049275..46051699-chr1:46215070..46217798,3	K562	blood:
48	chr1:45985173..45987673-chr1:46047489..46052049,5	MCF-7	breast:
49	chr1:46049302..46049898-chr9:20684213..20685119,2	NB4	blood:
50	chr1:45240107..45242701-chr1:46047468..46050316,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC17-5	chr1:46048539-46050383	NONHSAT002951

Variant related genes	Relation type
NASP	TF binding region
ENSG00000225447	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000137154	Chromatin interaction
ENSG00000103037	Chromatin interaction
ENSG00000140988	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000201801	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000186480	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000173660	Chromatin interaction
ENSG00000135709	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000132128	Chromatin interaction
ENSG00000255198	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000085999	Chromatin interaction
ENSG00000159596	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000227071	Chromatin interaction
ENSG00000196367	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000086015	Chromatin interaction
ENSG00000117481	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000197429	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000070759	Chromatin interaction
ENSG00000132334	Chromatin interaction
ENSG00000159588	Chromatin interaction
ENSG00000149485	Chromatin interaction
ENSG00000134824	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11590549	1.00[JPT][hapmap]
rs2275084	1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28365868	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28365913	1.00[EUR][1000 genomes]
rs3748645	0.88[JPT][hapmap];1.00[EUR][1000 genomes]
rs3811433	1.00[EUR][1000 genomes]
rs3811434	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269109	1.00[EUR][1000 genomes]
rs41269111	1.00[EUR][1000 genomes]
rs41269115	1.00[EUR][1000 genomes]
rs41272133	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41312018	1.00[EUR][1000 genomes]
rs56215132	1.00[EUR][1000 genomes]
rs56220330	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
4	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
5	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
6	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
7	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
8	esv3342998	chr1:46035908-46066462	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46048600-46051000	Active TSS	Colonic Mucosa	Colon
2	chr1:46048800-46049600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr1:46048800-46049600	Flanking Active TSS	Liver	Liver
4	chr1:46048800-46049800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:46048800-46050400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr1:46048800-46050600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:46048800-46050600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:46048800-46050600	Active TSS	Brain Anterior Caudate	brain
9	chr1:46048800-46050600	Active TSS	Brain Cingulate Gyrus	brain
10	chr1:46048800-46050600	Active TSS	Left Ventricle	heart
11	chr1:46048800-46050600	Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr1:46048800-46050600	Active TSS	NHEK	skin
13	chr1:46048800-46050800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:46048800-46050800	Active TSS	Muscle Satellite Cultured Cells	--
15	chr1:46048800-46050800	Active TSS	Brain Germinal Matrix	brain
16	chr1:46048800-46050800	Active TSS	Brain Hippocampus Middle	brain
17	chr1:46048800-46050800	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr1:46048800-46050800	Active TSS	Fetal Brain Female	brain
19	chr1:46048800-46050800	Active TSS	Rectal Smooth Muscle	rectum
20	chr1:46048800-46050800	Active TSS	HSMMtube	muscle
21	chr1:46048800-46050800	Active TSS	K562	blood
22	chr1:46048800-46050800	Active TSS	NH-A	brain
23	chr1:46048800-46051000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:46048800-46051000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:46048800-46051000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:46048800-46051000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr1:46048800-46051000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:46048800-46051000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:46048800-46051000	Active TSS	Fetal Stomach	stomach
30	chr1:46048800-46051000	Active TSS	Psoas Muscle	Psoas
31	chr1:46048800-46051000	Active TSS	Hela-S3	cervix
32	chr1:46048800-46051000	Active TSS	HSMM	muscle
33	chr1:46048800-46051000	Active TSS	NHLF	lung
34	chr1:46048800-46051200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:46048800-46051200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:46048800-46051200	Active TSS	Fetal Kidney	kidney
37	chr1:46048800-46051200	Active TSS	Right Ventricle	heart
38	chr1:46048800-46051200	Active TSS	NHDF-Ad	bronchial
39	chr1:46048800-46051400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:46048800-46051800	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr1:46048800-46051800	Active TSS	H1 Cell Line	embryonic stem cell
42	chr1:46048800-46052200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:46048800-46052200	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr1:46048800-46052400	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr1:46048800-46052600	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr1:46048800-46052600	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr1:46048800-46052800	Active TSS	H9 Cell Line	embryonic stem cell
48	chr1:46049000-46049800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr1:46049000-46050400	Active TSS	Primary monocytes fromperipheralblood	blood
50	chr1:46049000-46050400	Active TSS	Duodenum Mucosa	Duodenum

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