Variant report

Variant	rs56128678
Chromosome Location	chr12:57423197-57423198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57422175..57424146-chr12:57481515..57483170,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166886	Chromatin interaction
ENSG00000166881	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	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10400555	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1044939	0.91[AFR][1000 genomes];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	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[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17119301	0.90[ASN][1000 genomes]
rs17119327	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17119330	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17119344	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119352	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17119386	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17119388	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17119390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119407	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17119416	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17119418	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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270737	0.95[AFR][1000 genomes];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	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2371717	0.84[AFR][1000 genomes];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	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	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782330	0.95[AFR][1000 genomes];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	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4039	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4143085	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56270558	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56354404	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	0.91[AFR][1000 genomes];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	0.95[AFR][1000 genomes];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	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73114426	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73114428	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73114434	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73114436	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73114437	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73114446	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73114452	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73114457	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114459	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114467	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114468	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114472	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73116494	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73116501	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73118413	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	0.95[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]
rs755221	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956166	0.89[ASN][1000 genomes]
rs7961920	0.99[ASN][1000 genomes]
rs7962771	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7969312	0.89[ASN][1000 genomes]
rs7972615	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:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57413400-57425000	Weak transcription	Spleen	Spleen
2	chr12:57416800-57439400	Strong transcription	Fetal Intestine Small	intestine
3	chr12:57417200-57441200	Weak transcription	Small Intestine	intestine
4	chr12:57419200-57439400	Strong transcription	Duodenum Mucosa	Duodenum
5	chr12:57419800-57425000	Enhancers	Primary T cells from cord blood	blood
6	chr12:57419800-57426000	Enhancers	Primary T cells fromperipheralblood	blood
7	chr12:57419800-57426000	Enhancers	Fetal Thymus	thymus
8	chr12:57419800-57426200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr12:57419800-57439600	Strong transcription	Fetal Intestine Large	intestine
10	chr12:57420000-57440000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr12:57420400-57424800	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:57420400-57425000	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr12:57420400-57471800	Weak transcription	Gastric	stomach
14	chr12:57420800-57426000	Enhancers	Thymus	Thymus
15	chr12:57421000-57423200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:57421200-57424800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:57421200-57425000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:57421400-57425000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:57421600-57424200	Strong transcription	Colonic Mucosa	Colon
20	chr12:57421600-57424800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:57421600-57425000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr12:57421600-57425200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:57421800-57424600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr12:57421800-57425000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr12:57421800-57441600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:57422000-57424200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:57422000-57424200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:57422000-57424800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr12:57422000-57424800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:57422000-57424800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:57422000-57424800	Weak transcription	GM12878-XiMat	blood
32	chr12:57422000-57425000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr12:57422000-57425000	Weak transcription	Stomach Mucosa	stomach
34	chr12:57422000-57425400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:57422200-57424400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr12:57422200-57424600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:57422400-57423400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr12:57422400-57423600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr12:57422600-57424000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr12:57422600-57424400	Weak transcription	Brain Germinal Matrix	brain
41	chr12:57422600-57424800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr12:57422600-57425000	Weak transcription	K562	blood
43	chr12:57422800-57424600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:57422800-57425000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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