Variant report

Variant	rs12528843
Chromosome Location	chr6:30778403-30778404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30778242..30780250-chr6:30790501..30792302,2	K562	blood:
2	chr6:30582861..30585140-chr6:30778176..30780567,2	MCF-7	breast:
3	chr11:65196773..65198444-chr6:30776938..30778941,2	MCF-7	breast:
4	chr6:30775890..30781762-chr6:30785090..30789723,9	MCF-7	breast:
5	chr6:30766009..30775294-chr6:30775700..30782710,15	MCF-7	breast:
6	chr6:30693275..30696224-chr6:30778287..30780136,2	K562	blood:
7	chr6:30765847..30772235-chr6:30775518..30781372,10	K562	blood:
8	chr6:30703666..30722133-chr6:30776009..30801352,184	MCF-7	breast:
9	chr6:30456417..30458874-chr6:30776787..30780179,3	K562	blood:
10	chr6:30777372..30779783-chr6:30849270..30851072,2	K562	blood:
11	chr6:30708338..30713459-chr6:30777538..30783709,13	K562	blood:
12	chr6:30687859..30690544-chr6:30777327..30780060,3	MCF-7	breast:
13	chr6:30687466..30692169-chr6:30775918..30784078,7	K562	blood:
14	chr6:30749778..30751326-chr6:30778307..30780023,3	MCF-7	breast:
15	chr6:30778063..30780102-chr8:113652986..113654698,2	MCF-7	breast:
16	chr6:30767146..30768720-chr6:30776918..30779090,2	MCF-7	breast:
17	chr6:30706744..30716171-chr6:30774931..30783832,28	MCF-7	breast:
18	chr6:30777633..30780399-chr6:30780437..30782571,2	MCF-7	breast:
19	chr6:30716968..30722090-chr6:30774929..30783584,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000137331	Chromatin interaction
ENSG00000263608	Chromatin interaction
ENSG00000204592	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000201988	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000272540	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10947100	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10947101	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10947102	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12525494	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12661685	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13191291	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13191728	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13198118	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13201384	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13213083	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13213098	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13213469	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2269854	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2394403	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28744185	0.80[AFR][1000 genomes]
rs28744190	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3888583	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4248149	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4483030	0.83[EUR][1000 genomes]
rs4587207	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711234	0.82[EUR][1000 genomes]
rs4711237	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4713380	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4713381	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4713382	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713383	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713384	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713385	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713389	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713392	0.85[AFR][1000 genomes]
rs4947289	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4947290	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6901761	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6901776	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6905957	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7751827	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7751869	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295917	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295918	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295920	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9368640	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9368644	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9378108	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9378109	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9378148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9378224	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9380189	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9380190	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380191	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380193	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380194	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9380195	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380198	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9391692	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9391693	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9391694	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9391695	0.98[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9391696	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9391810	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9391811	0.90[AFR][1000 genomes]
rs9391812	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9394014	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9404970	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9404973	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9404974	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9404975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9405014	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
8	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
9	nsv884105	chr6:30775579-30786676	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv884106	chr6:30775579-30787323	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv884107	chr6:30776483-30787323	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30761600-30781000	Weak transcription	Small Intestine	intestine
2	chr6:30767200-30781200	Weak transcription	Gastric	stomach
3	chr6:30773000-30778600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:30774800-30779800	Weak transcription	HepG2	liver
5	chr6:30775000-30778600	Weak transcription	Placenta	Placenta
6	chr6:30776200-30779000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr6:30776400-30779000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr6:30776400-30783200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr6:30776400-30783400	Enhancers	Primary T cells fromperipheralblood	blood
10	chr6:30776600-30779800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr6:30776600-30780000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr6:30776600-30783400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr6:30776800-30779000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:30777000-30780400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:30777200-30779000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr6:30777200-30779000	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr6:30777200-30779000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr6:30777200-30779200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:30777200-30781000	Enhancers	K562	blood
20	chr6:30777200-30783200	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr6:30777400-30778600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:30777400-30779000	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr6:30777400-30779200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr6:30777400-30780400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:30777600-30778600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:30777600-30778600	Weak transcription	Colonic Mucosa	Colon
27	chr6:30777600-30780200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:30777600-30780400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr6:30777800-30779800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:30778000-30778600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:30778000-30779000	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr6:30778000-30779000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr6:30778000-30779200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr6:30778000-30779200	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr6:30778000-30779200	Enhancers	Primary B cells from cord blood	blood
36	chr6:30778000-30780000	Enhancers	HMEC	breast
37	chr6:30778200-30778600	Flanking Active TSS	NHEK	skin
38	chr6:30778200-30779000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:30778200-30779000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr6:30778200-30779000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr6:30778200-30779000	Flanking Active TSS	GM12878-XiMat	blood
42	chr6:30778200-30779200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:30778200-30779800	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr6:30778200-30780400	Enhancers	Primary T cells from cord blood	blood
45	chr6:30778400-30778600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:30778400-30779000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:30778400-30779000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:30778400-30779000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:30778400-30779200	Enhancers	Primary B cells from peripheral blood	blood
50	chr6:30778400-30779200	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links