Variant report

Variant	rs755221
Chromosome Location	chr12:57425146-57425147
allele	A/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	RCOR1	chr12:57425018-57425174	K562	blood:	n/a	n/a
2	ELF1	chr12:57424833-57425195	K562	blood:	n/a	chr12:57425043-57425054 chr12:57425000-57425013 chr12:57425042-57425055
3	NFIC	chr12:57425093-57425625	ECC-1	luminal epithelium:	n/a	chr12:57425332-57425348 chr12:57425332-57425349
4	REST	chr12:57425113-57425642	MCF-7	breast:	n/a	n/a
5	RAD21	chr12:57425119-57425437	HepG2	liver:	n/a	n/a
6	MYC	chr12:57424882-57425271	NB4	blood:	n/a	n/a
7	CTCF	chr12:57425146-57425487	GM12878	blood:	n/a	chr12:57425298-57425316
8	RAD21	chr12:57425076-57425541	ECC-1	luminal epithelium:	n/a	n/a
9	RAD21	chr12:57425021-57425599	MCF-7	breast:	n/a	n/a
10	TCF7L2	chr12:57424838-57425380	HCT-116	colon:	n/a	chr12:57425040-57425047 chr12:57425038-57425047
11	CTCF	chr12:57425139-57425403	K562	blood:	n/a	chr12:57425298-57425316
12	YY1	chr12:57425131-57425415	GM12891	blood:	n/a	n/a
13	TCF7L2	chr12:57424874-57425215	Hela-S3	cervix:	n/a	chr12:57425040-57425047 chr12:57425038-57425047
14	RAD21	chr12:57425130-57425411	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZNF263	chr12:57425069-57425425	HEK293-T-REx	kidney:	n/a	n/a
16	SP1	chr12:57424894-57425423	GM12878	blood:	n/a	n/a
17	RAD21	chr12:57425029-57425583	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr12:57424979-57425179	NB4	blood:	n/a	n/a
19	RAD21	chr12:57425088-57425524	HepG2	liver:	n/a	n/a
20	SPI1	chr12:57424817-57425251	HL-60	blood:	n/a	chr12:57425043-57425056 chr12:57425042-57425055

No.	Distal block	Cell Line	Cell type
1	chr12:57399976..57400833-chr12:57424825..57425490,2	MCF-7	breast:
2	chr12:57424729..57426887-chr12:57432611..57435590,2	K562	blood:
3	chr12:57419477..57423576-chr12:57424923..57428505,3	K562	blood:

Variant related genes	Relation type
TAC3	TF binding region
MYO1A	TF binding region
ENSG00000166860	Chromatin interaction
ENSG00000166863	Chromatin interaction
ENSG00000166866	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10400412	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10400555	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1044939	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10506347	0.83[AMR][1000 genomes]
rs10506350	0.91[ASN][1000 genomes]
rs10506351	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1072670	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11832487	0.89[ASN][1000 genomes]
rs11834851	0.89[ASN][1000 genomes]
rs11834856	0.89[ASN][1000 genomes]
rs11836517	0.89[ASN][1000 genomes]
rs12099695	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12810024	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12810837	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12812499	0.90[ASN][1000 genomes]
rs12815538	0.89[ASN][1000 genomes]
rs12818342	0.89[ASN][1000 genomes]
rs12824682	0.89[ASN][1000 genomes]
rs12827039	0.89[ASN][1000 genomes]
rs12827286	0.85[ASN][1000 genomes]
rs1552245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17119301	0.90[ASN][1000 genomes]
rs17119327	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17119330	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17119344	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17119386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17119388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17119390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119407	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17119416	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17119418	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1843311	0.89[ASN][1000 genomes]
rs1843312	0.89[ASN][1000 genomes]
rs1843313	0.89[ASN][1000 genomes]
rs2035545	0.83[ASN][1000 genomes]
rs2167306	0.89[ASN][1000 genomes]
rs2233267	0.82[ASN][1000 genomes]
rs2270736	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270737	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270739	0.99[ASN][1000 genomes]
rs2279373	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2279743	0.90[ASN][1000 genomes]
rs2291855	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2371717	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28589663	0.89[ASN][1000 genomes]
rs2888139	0.90[ASN][1000 genomes]
rs34186462	0.89[ASN][1000 genomes]
rs34253098	0.89[ASN][1000 genomes]
rs34359134	0.89[ASN][1000 genomes]
rs34762603	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34969650	0.91[ASN][1000 genomes]
rs35034299	0.89[ASN][1000 genomes]
rs35243318	0.89[ASN][1000 genomes]
rs35493121	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35937600	0.83[ASN][1000 genomes]
rs3759134	0.81[ASN][1000 genomes]
rs3759135	0.82[ASN][1000 genomes]
rs3782329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782330	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3803018	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3894415	0.90[ASN][1000 genomes]
rs4016338	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4039	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4143085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56128678	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56270558	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56354404	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57056392	0.99[ASN][1000 genomes]
rs57129030	0.89[ASN][1000 genomes]
rs57351760	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs57558853	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58298943	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58389529	0.97[ASN][1000 genomes]
rs60258120	0.88[ASN][1000 genomes]
rs60273384	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60380217	0.89[ASN][1000 genomes]
rs61504157	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66741626	0.83[ASN][1000 genomes]
rs67476535	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67771054	0.89[ASN][1000 genomes]
rs67844278	0.90[ASN][1000 genomes]
rs68126184	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs697222	0.90[ASN][1000 genomes]
rs7135297	0.91[ASN][1000 genomes]
rs7136770	0.90[ASN][1000 genomes]
rs71461303	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72482268	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7298475	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73114426	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73114428	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73114434	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73114436	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73114437	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73114446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73114452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73114457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114467	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114472	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73116494	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73116501	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73118413	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73118416	0.82[ASN][1000 genomes]
rs73118418	0.82[ASN][1000 genomes]
rs73131120	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs733629	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs746049	0.89[ASN][1000 genomes]
rs7487948	0.89[ASN][1000 genomes]
rs754398	0.94[ASN][1000 genomes]
rs7956166	0.89[ASN][1000 genomes]
rs7961920	0.99[ASN][1000 genomes]
rs7962771	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7969312	0.89[ASN][1000 genomes]
rs7972615	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs901068	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899110	chr12:57422934-57472502	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57416800-57439400	Strong transcription	Fetal Intestine Small	intestine
2	chr12:57417200-57441200	Weak transcription	Small Intestine	intestine
3	chr12:57419200-57439400	Strong transcription	Duodenum Mucosa	Duodenum
4	chr12:57419800-57426000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr12:57419800-57426000	Enhancers	Fetal Thymus	thymus
6	chr12:57419800-57426200	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr12:57419800-57439600	Strong transcription	Fetal Intestine Large	intestine
8	chr12:57420000-57440000	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr12:57420400-57471800	Weak transcription	Gastric	stomach
10	chr12:57420800-57426000	Enhancers	Thymus	Thymus
11	chr12:57421600-57425200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:57421800-57441600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:57422000-57425400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:57423400-57426200	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr12:57423800-57426200	Enhancers	Dnd41	blood
16	chr12:57424000-57425200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:57424200-57431400	Weak transcription	Fetal Stomach	stomach
18	chr12:57424200-57431600	Weak transcription	Colonic Mucosa	Colon
19	chr12:57424400-57425400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:57424400-57426000	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr12:57424400-57426400	Enhancers	Brain Germinal Matrix	brain
22	chr12:57424600-57425600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr12:57424600-57425600	Enhancers	Primary hematopoietic stem cells	blood
24	chr12:57424600-57425600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr12:57424600-57425800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:57424800-57425200	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr12:57424800-57425200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr12:57424800-57425400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:57424800-57425400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:57424800-57425400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:57424800-57425600	Enhancers	Primary B cells from peripheral blood	blood
32	chr12:57424800-57425600	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr12:57424800-57425600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:57424800-57425800	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr12:57424800-57425800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:57424800-57425800	Enhancers	A549	lung
37	chr12:57424800-57426000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:57424800-57426000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:57424800-57426000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr12:57424800-57426000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:57424800-57426000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:57424800-57426200	Enhancers	HMEC	breast
43	chr12:57424800-57427400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:57424800-57427800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:57425000-57425200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:57425000-57425200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:57425000-57425200	Enhancers	Spleen	Spleen
48	chr12:57425000-57425400	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr12:57425000-57425400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr12:57425000-57425400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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