Variant report

Variant	rs1000423
Chromosome Location	chr17:59475642-59475643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:46)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:59475361-59477382	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr17:59468390-59479830	ProgFib	skin:	n/a	n/a
3	MYBL2	chr17:59475510-59476128	HepG2	liver:	n/a	n/a
4	SUZ12	chr17:59473583-59483306	NT2-D1	testis:	n/a	n/a
5	MXI1	chr17:59473914-59480739	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr17:59474725-59477471	SK-N-SH	brain:	n/a	n/a
7	MAZ	chr17:59472821-59478277	IMR90	lung:	n/a	chr17:59474298-59474308 chr17:59475824-59475831 chr17:59474536-59474546 chr17:59474205-59474214
8	HDAC2	chr17:59474717-59482617	MCF-7	breast:	n/a	chr17:59476354-59476363 chr17:59480823-59480832
9	MAX	chr17:59474780-59476444	SK-N-SH	brain:	n/a	chr17:59475824-59475831
10	CTBP2	chr17:59474838-59477174	H1-hESC	embryonic stem cell:	n/a	n/a
11	TEAD4	chr17:59474770-59479769	A549	lung:	n/a	n/a
12	SIN3AK20	chr17:59474247-59476463	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr17:59473262-59482475	IMR90	lung:	n/a	n/a
14	TAF1	chr17:59475558-59476070	SK-N-SH	brain:	n/a	n/a
15	MAX	chr17:59475547-59478525	HepG2	liver:	n/a	chr17:59475824-59475831
16	SUZ12	chr17:59474806-59476895	H1-hESC	embryonic stem cell:	n/a	n/a
17	MXI1	chr17:59473244-59478459	IMR90	lung:	n/a	n/a
18	RAD21	chr17:59474328-59477891	IMR90	lung:	n/a	chr17:59476606-59476616 chr17:59475048-59475062 chr17:59476563-59476576 chr17:59474744-59474754 chr17:59475436-59475445
19	MAX	chr17:59474705-59482813	MCF-7	breast:	n/a	chr17:59480404-59480414 chr17:59475824-59475831 chr17:59479783-59479793 chr17:59480615-59480622
20	MAX	chr17:59474370-59476475	SK-N-SH	brain:	n/a	chr17:59475824-59475831 chr17:59474536-59474546
21	POLR2A	chr17:59474879-59476799	H1-neurons	neurons:	n/a	n/a
22	GATA3	chr17:59474967-59477350	MCF-7	breast:	n/a	chr17:59475873-59475883
23	TAF1	chr17:59475369-59475855	SK-N-SH	brain:	n/a	n/a
24	CTCF	chr17:59475620-59475770	SK-N-SH_RA	brain:	n/a	n/a
25	REST	chr17:59475191-59475832	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr17:59474874-59476582	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr17:59473895-59476435	SK-N-SH	brain:	n/a	n/a

No data

(count:46 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59474412..59476108-chr20:52481688..52483520,2	MCF-7	breast:
2	chr17:59474707..59482954-chr20:45984179..45991970,21	MCF-7	breast:
3	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
4	chr17:57914760..57924876-chr17:59472133..59480361,28	MCF-7	breast:
5	chr17:57918266..57925909-chr17:59474699..59479743,11	MCF-7	breast:
6	chr17:59468937..59480240-chr20:49340039..49356868,49	MCF-7	breast:
7	chr17:59468469..59482635-chr20:45977748..45992950,51	MCF-7	breast:
8	chr17:59474205..59475906-chr20:45845808..45848443,2	MCF-7	breast:
9	chr17:59475321..59478062-chr9:127629865..127632518,2	MCF-7	breast:
10	chr1:226110432..226113669-chr17:59475384..59478027,3	MCF-7	breast:
11	chr17:56706858..56710627-chr17:59472052..59479583,11	MCF-7	breast:
12	chr16:89786416..89788600-chr17:59475587..59477647,2	MCF-7	breast:
13	chr17:59474624..59476762-chr20:62370265..62372369,2	MCF-7	breast:
14	chr17:59473100..59476327-chr17:59937643..59941414,3	MCF-7	breast:
15	chr1:113162339..113164666-chr17:59475031..59477488,2	MCF-7	breast:
16	chr1:173835625..173838583-chr17:59475360..59477954,2	MCF-7	breast:
17	chr17:56735328..56738474-chr17:59474554..59477882,3	MCF-7	breast:
18	chr16:71405742..71407571-chr17:59474324..59476881,2	MCF-7	breast:
19	chr17:59475358..59477997-chr20:52197460..52200356,2	MCF-7	breast:
20	chr17:59475016..59476729-chr20:52744400..52746392,3	MCF-7	breast:
21	chr11:61193958..61196849-chr17:59473654..59475823,2	MCF-7	breast:
22	chr17:59473508..59476352-chr2:219187700..219189664,2	MCF-7	breast:
23	chr17:59475424..59477286-chr9:130741425..130743853,3	MCF-7	breast:
24	chr17:59473116..59475662-chr20:49369378..49372060,2	MCF-7	breast:
25	chr17:59475592..59478154-chr9:33076003..33078160,2	MCF-7	breast:
26	chr17:59475037..59478844-chr20:46130288..46133221,4	MCF-7	breast:
27	chr11:62607389..62609946-chr17:59474359..59478741,7	MCF-7	breast:
28	chr17:59474584..59479937-chr20:48725175..48731303,15	MCF-7	breast:
29	chr12:2985197..2987791-chr17:59475182..59478141,2	MCF-7	breast:
30	chr1:112539326..112541454-chr17:59474271..59475932,2	MCF-7	breast:
31	chr16:89988336..89991166-chr17:59475068..59476878,2	MCF-7	breast:
32	chr17:59475479..59478069-chr6:26030840..26033823,3	MCF-7	breast:
33	chr17:59475519..59479534-chr20:45977874..45982127,5	MCF-7	breast:
34	chr17:59474996..59480161-chr20:52556121..52561884,6	MCF-7	breast:
35	chr17:59475462..59478386-chr17:59485811..59488031,27	MCF-7	breast:
36	chr17:59468167..59483990-chr20:49341590..49352501,35	MCF-7	breast:
37	chr1:112530336..112534122-chr17:59473481..59479325,11	MCF-7	breast:
38	chr17:59472839..59476239-chr3:161133074..161135554,3	MCF-7	breast:
39	chr17:59474806..59476625-chr20:45952325..45954031,2	MCF-7	breast:
40	chr17:59474608..59482837-chr20:48728341..48732502,9	MCF-7	breast:
41	chr1:115299188..115301953-chr17:59475325..59477891,2	MCF-7	breast:
42	chr17:59475062..59478026-chr20:39655651..39657666,2	MCF-7	breast:
43	chr1:112531113..112535796-chr17:59474143..59479478,11	MCF-7	breast:
44	chr17:59473576..59476219-chr7:75934153..75935761,2	MCF-7	breast:
45	chr17:59096898..59099247-chr17:59473904..59475834,2	MCF-7	breast:
46	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NACA2-2	chr17:59475373-59476044	NONHSAT055129

No data

Variant related genes	Relation type
TBX2	TF binding region
ENSG00000267280	TF binding region
ENSG00000062716	Chromatin interaction
ENSG00000273451	Chromatin interaction
ENSG00000171385	Chromatin interaction
ENSG00000143811	Chromatin interaction
ENSG00000078246	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000127838	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000122692	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000244687	Chromatin interaction
ENSG00000075399	Chromatin interaction
ENSG00000149532	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000124243	Chromatin interaction
ENSG00000231119	Chromatin interaction
ENSG00000136950	Chromatin interaction
ENSG00000125520	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000158805	Chromatin interaction
ENSG00000172137	Chromatin interaction
ENSG00000124151	Chromatin interaction
ENSG00000231437	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000111206	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000171792	Chromatin interaction
ENSG00000198900	Chromatin interaction
ENSG00000009307	Chromatin interaction
ENSG00000259006	Chromatin interaction
ENSG00000167106	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000256591	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000258947	Chromatin interaction
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1057987	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1058004	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10853031	0.82[ASN][1000 genomes]
rs11868532	0.86[ASN][1000 genomes]
rs11871637	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12952625	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240736	0.97[EUR][1000 genomes]
rs2270114	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2286526	0.94[EUR][1000 genomes]
rs34446110	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62071306	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7215775	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs729781	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8068318	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8073698	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8074151	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8078036	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9891115	0.82[ASN][1000 genomes]
rs9905140	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065939	chr17:59283350-59517730	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	331 gene(s)	inside rSNPs	diseases
2	nsv833505	chr17:59323466-59518007	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	326 gene(s)	inside rSNPs	diseases
3	nsv833506	chr17:59362377-59562984	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
4	nsv518130	chr17:59456589-59491281	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	265 gene(s)	inside rSNPs	diseases
5	esv1796927	chr17:59460119-59495319	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	270 gene(s)	inside rSNPs	diseases
6	nsv908663	chr17:59464069-59521310	Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	278 gene(s)	inside rSNPs	diseases
7	nsv908664	chr17:59465697-59491030	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	261 gene(s)	inside rSNPs	diseases
8	nsv908665	chr17:59470193-59494574	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
9	nsv908666	chr17:59470842-59489822	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	253 gene(s)	inside rSNPs	diseases
10	nsv908667	chr17:59471151-59491030	Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	256 gene(s)	inside rSNPs	diseases
11	nsv908668	chr17:59471151-59494574	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	263 gene(s)	inside rSNPs	diseases
12	nsv908669	chr17:59471372-59491030	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	255 gene(s)	inside rSNPs	diseases
13	nsv908670	chr17:59471372-59494574	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	262 gene(s)	inside rSNPs	diseases
14	esv3374888	chr17:59473395-59475943	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59470800-59476000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr17:59472600-59475800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr17:59473000-59476000	Bivalent/Poised TSS	Fetal Lung	lung
4	chr17:59473400-59476200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr17:59473400-59476200	Bivalent/Poised TSS	Psoas Muscle	Psoas
6	chr17:59473400-59476400	Bivalent Enhancer	Brain Germinal Matrix	brain
7	chr17:59473400-59477000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr17:59473400-59479800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr17:59473600-59476200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:59473600-59476400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
11	chr17:59473600-59477400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
12	chr17:59473800-59476000	Bivalent Enhancer	Spleen	Spleen
13	chr17:59473800-59476200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr17:59473800-59476200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr17:59474000-59476200	Bivalent/Poised TSS	Fetal Kidney	kidney
16	chr17:59474000-59476200	Bivalent Enhancer	Stomach Mucosa	stomach
17	chr17:59474000-59476200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
18	chr17:59474200-59476000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
19	chr17:59474200-59476200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
20	chr17:59474200-59476200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr17:59474200-59476400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
22	chr17:59474200-59479000	Active TSS	Aorta	Aorta
23	chr17:59474200-59481000	Active TSS	NHDF-Ad	bronchial
24	chr17:59474400-59475800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr17:59474400-59476200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr17:59474400-59479800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr17:59474600-59476400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
28	chr17:59474800-59475800	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
29	chr17:59474800-59476000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
30	chr17:59474800-59476400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr17:59474800-59476600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
32	chr17:59474800-59476600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
33	chr17:59474800-59476800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
34	chr17:59474800-59477200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
35	chr17:59474800-59477200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
36	chr17:59474800-59477200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
37	chr17:59474800-59477200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
38	chr17:59474800-59477400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
39	chr17:59475000-59475800	Bivalent Enhancer	Fetal Brain Female	brain
40	chr17:59475000-59475800	Flanking Active TSS	HepG2	liver
41	chr17:59475000-59476000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr17:59475000-59476000	Bivalent/Poised TSS	HSMMtube	muscle
43	chr17:59475000-59476200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
44	chr17:59475000-59476200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
45	chr17:59475000-59476200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr17:59475000-59476200	Bivalent Enhancer	Liver	Liver
47	chr17:59475000-59476200	Bivalent Enhancer	Brain Substantia Nigra	brain
48	chr17:59475000-59476400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr17:59475000-59476400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr17:59475000-59476400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood

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