Variant report

Variant	rs12722725
Chromosome Location	chr1:113258681-113258682
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	MTA3	chr1:113258405-113259187	GM12878	blood:	n/a	n/a
2	WRNIP1	chr1:113258670-113259286	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:113258681-113259232	H1-neurons	neurons:	n/a	n/a
4	REST	chr1:113257894-113259461	H1-neurons	neurons:	n/a	chr1:113259138-113259147
5	RAD21	chr1:113258656-113259475	MCF-7	breast:	n/a	chr1:113259182-113259192 chr1:113259064-113259083
6	CTCF	chr1:113258567-113259306	K562	blood:	n/a	chr1:113259066-113259075 chr1:113259063-113259081
7	NR2F2	chr1:113257947-113259302	K562	blood:	n/a	n/a
8	SIN3A	chr1:113256279-113259295	H1-hESC	embryonic stem cell:	n/a	chr1:113258039-113258050
9	CTCF	chr1:113258654-113259407	HCT-116	colon:	n/a	chr1:113259066-113259075 chr1:113259063-113259081
10	SMARCB1	chr1:113257643-113259090	Hela-S3	cervix:	n/a	n/a
11	RAD21	chr1:113258008-113259681	SK-N-SH	brain:	n/a	chr1:113259182-113259192 chr1:113258179-113258191 chr1:113259064-113259083
12	RAD21	chr1:113258451-113259489	HCT-116	colon:	n/a	chr1:113259182-113259192 chr1:113259064-113259083
13	SMC3	chr1:113258561-113259379	GM12878	blood:	n/a	chr1:113259065-113259079
14	CTCF	chr1:113258011-113259506	A549	lung:	n/a	chr1:113259066-113259075 chr1:113259063-113259081
15	CTCF	chr1:113258560-113258710	GM12873	blood:	n/a	n/a
16	MAZ	chr1:113257047-113259476	IMR90	lung:	n/a	chr1:113257988-113257997
17	SMC3	chr1:113258668-113259298	Hela-S3	cervix:	n/a	chr1:113259065-113259079
18	ZNF263	chr1:113258192-113259345	HEK293-T-REx	kidney:	n/a	chr1:113258943-113258952 chr1:113258945-113258966 chr1:113258993-113259014
19	ZNF384	chr1:113258677-113259195	K562	blood:	n/a	n/a
20	CTCF	chr1:113258024-113259531	HCT-116	colon:	n/a	chr1:113259066-113259075 chr1:113259063-113259081
21	MAZ	chr1:113257300-113259261	K562	blood:	n/a	chr1:113257988-113257997
22	CTCF	chr1:113256493-113259631	SK-N-SH	brain:	n/a	chr1:113259066-113259075 chr1:113259063-113259081
23	ARID3A	chr1:113258629-113259125	HepG2	liver:	n/a	n/a
24	SMARCC1	chr1:113258131-113259388	Hela-S3	cervix:	n/a	n/a
25	RAD21	chr1:113258673-113259514	IMR90	lung:	n/a	chr1:113259182-113259192 chr1:113259064-113259083
26	RAD21	chr1:113258651-113259315	Hela-S3	cervix:	n/a	chr1:113259182-113259192 chr1:113259064-113259083
27	POLR2A	chr1:113257948-113258688	H1-neurons	neurons:	n/a	n/a
28	RAD21	chr1:113258628-113259522	HCT-116	colon:	n/a	chr1:113259182-113259192 chr1:113259064-113259083
29	CTCF	chr1:113258580-113258730	AG10803	skin:	n/a	n/a
30	SMC3	chr1:113257963-113259603	SK-N-SH	brain:	n/a	chr1:113259065-113259079
31	BRCA1	chr1:113258527-113259228	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:113160555..113166228-chr1:113255932..113262161,8	K562	blood:
2	chr1:113258144..113259666-chr1:113261465..113263910,2	K562	blood:
3	chr1:113257176..113260368-chr1:113260579..113263250,3	K562	blood:
4	chr1:113257532..113261488-chr1:113614794..113617265,4	K562	blood:
5	chr1:113160602..113163896-chr1:113252357..113259247,7	K562	blood:
6	chr1:113257309..113258998-chr1:114446539..114449479,2	K562	blood:
7	chr1:113258665..113259418-chrX:71573090..71573646,2	MCF-7	breast:
8	chr1:113215712..113221627-chr1:113253708..113259381,5	MCF-7	breast:
9	chr1:113254236..113255978-chr1:113257610..113260572,2	MCF-7	breast:
10	chr1:113253460..113256284-chr1:113256871..113259194,3	MCF-7	breast:
11	chr1:113239573..113244483-chr1:113252369..113259292,10	K562	blood:
12	chr1:113160638..113164364-chr1:113256565..113260015,7	MCF-7	breast:
13	chr1:113255626..113260544-chr1:113496476..113500122,4	K562	blood:
14	chr1:113258681..113259438-chr1:113351567..113352234,2	MCF-7	breast:
15	chr1:113258208..113260404-chr1:113615515..113617358,3	MCF-7	breast:
16	chr1:112933134..112934137-chr1:113258448..113259503,5	K562	blood:
17	chr1:113160649..113163501-chr1:113258154..113260079,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM19A3-1	chr1:113258294-113260418	ENSG00000261595.1
2	lnc-FAM19A3-1	chr1:113258294-113260434	NONHSAT005280

Variant related genes	Relation type
FAM19A3	TF binding region
PPM1J	TF binding region
ENSG00000271810	TF binding region
ENSG00000238198	Chromatin interaction
ENSG00000271810	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000155380	Chromatin interaction
ENSG00000184599	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000226419	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000198799	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12722910	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724682	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12729635	1.00[ASN][1000 genomes]
rs12736457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12737053	1.00[ASN][1000 genomes]
rs34611728	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34731458	1.00[ASN][1000 genomes]
rs34961977	1.00[ASN][1000 genomes]
rs351366	1.00[ASN][1000 genomes]
rs35735679	1.00[ASN][1000 genomes]
rs35995150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36087180	1.00[ASN][1000 genomes]
rs61818824	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61818825	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61818828	1.00[ASN][1000 genomes]
rs6688050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71659381	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers 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 miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	esv18511	chr1:113246318-113350775	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv998794	chr1:113246630-113310418	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	nsv872157	chr1:113247467-113265819	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv547566	chr1:113248365-113301657	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
12	nsv872158	chr1:113250888-113265819	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv872159	chr1:113252091-113265819	Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113256200-113259000	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr1:113256400-113259000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:113256400-113259200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:113256600-113258800	Active TSS	Psoas Muscle	Psoas
5	chr1:113256600-113259000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr1:113256600-113259000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:113256600-113259000	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr1:113256600-113259000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr1:113256600-113259200	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr1:113256600-113259200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:113256800-113258800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:113256800-113258800	Active TSS	Placenta Amnion	Placenta Amnion
13	chr1:113256800-113259000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:113256800-113259000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:113256800-113259000	Active TSS	Aorta	Aorta
16	chr1:113257000-113258800	Active TSS	A549	lung
17	chr1:113257000-113259000	Active TSS	Left Ventricle	heart
18	chr1:113257000-113259200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:113257200-113259000	Active TSS	Ovary	ovary
20	chr1:113257400-113259200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:113257600-113258800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:113257600-113259000	Active TSS	Gastric	stomach
23	chr1:113257600-113259000	Active TSS	Right Ventricle	heart
24	chr1:113258000-113259000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:113258200-113258800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:113258200-113258800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:113258200-113258800	Flanking Active TSS	Colonic Mucosa	Colon
28	chr1:113258200-113258800	Active TSS	Fetal Brain Male	brain
29	chr1:113258200-113258800	Flanking Active TSS	Rectal Smooth Muscle	rectum
30	chr1:113258200-113259000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:113258200-113259000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr1:113258200-113259000	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr1:113258200-113259000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:113258200-113259000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr1:113258200-113259000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:113258200-113259000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:113258200-113259000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr1:113258200-113259000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:113258200-113259000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr1:113258200-113259000	Flanking Active TSS	Liver	Liver
41	chr1:113258200-113259000	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr1:113258200-113259000	Flanking Active TSS	Fetal Intestine Small	intestine
43	chr1:113258200-113259000	Flanking Active TSS	Placenta	Placenta
44	chr1:113258200-113259000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
45	chr1:113258200-113259000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr1:113258200-113259000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr1:113258200-113259000	Flanking Active TSS	Stomach Mucosa	stomach
48	chr1:113258200-113259000	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr1:113258200-113259000	Flanking Active TSS	HMEC	breast
50	chr1:113258200-113259000	Flanking Active TSS	HUVEC	blood vessel

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