Variant report

Variant	rs1619653
Chromosome Location	chr12:56426577-56426578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56421691..56428762-chr12:56433229..56437460,13	MCF-7	breast:
2	chr12:56364792..56367308-chr12:56426330..56428139,2	K562	blood:
3	chr12:56422020..56423685-chr12:56426127..56428274,2	K562	blood:
4	chr12:56424810..56427622-chr12:56435520..56438792,3	K562	blood:

Variant related genes	Relation type
ENSG00000197728	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000123374	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11171736	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1581007	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1689507	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1689516	0.85[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1701705	0.85[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1702870	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1702871	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1702875	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1995742	1.00[MEX][hapmap]
rs2452822	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2452826	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2456445	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2456446	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2456969	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2629449	1.00[MEX][hapmap]
rs35382885	1.00[MEX][hapmap]
rs705706	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7301099	1.00[MEX][hapmap];0.80[MKK][hapmap]
rs7309340	0.81[AFR][1000 genomes]
rs7310325	1.00[MEX][hapmap]
rs772917	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs772924	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs772925	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs772926	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs773118	0.87[AFR][1000 genomes]
rs773644	1.00[MEX][hapmap]
rs7977521	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs808896	0.85[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs808905	0.82[AFR][1000 genomes]
rs9645818	0.85[AFR][1000 genomes]
rs9738150	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv1067906	chr12:56424828-56445284	Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56402200-56434800	Weak transcription	Psoas Muscle	Psoas
2	chr12:56409400-56435000	Weak transcription	Stomach Mucosa	stomach
3	chr12:56416000-56434800	Weak transcription	Primary B cells from cord blood	blood
4	chr12:56416000-56434800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr12:56416000-56435000	Weak transcription	Right Atrium	heart
6	chr12:56416200-56434800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:56416400-56431000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:56416600-56431000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:56417400-56430800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:56417800-56430600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:56418000-56431000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:56418200-56427200	Strong transcription	K562	blood
13	chr12:56418200-56432600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:56418400-56432000	Strong transcription	Brain Germinal Matrix	brain
15	chr12:56418400-56432800	Strong transcription	Fetal Brain Female	brain
16	chr12:56418400-56433000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:56418600-56431400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:56418600-56433200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:56421200-56430000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:56421800-56426800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:56421800-56428400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:56421800-56434600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:56423000-56429800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:56423200-56429800	Strong transcription	Fetal Kidney	kidney
25	chr12:56423200-56431400	Strong transcription	Fetal Muscle Leg	muscle
26	chr12:56423200-56431600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr12:56423400-56433000	Strong transcription	Fetal Intestine Large	intestine
28	chr12:56423600-56433400	Strong transcription	Fetal Stomach	stomach
29	chr12:56423600-56434400	Weak transcription	HMEC	breast
30	chr12:56423600-56434800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:56423600-56434800	Weak transcription	NH-A	brain
32	chr12:56423800-56433200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:56423800-56434000	Weak transcription	NHEK	skin
34	chr12:56424600-56432800	Strong transcription	Placenta	Placenta
35	chr12:56424600-56433200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:56424600-56433200	Strong transcription	Fetal Lung	lung
37	chr12:56425000-56430000	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:56425000-56430400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:56425000-56431400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr12:56425000-56431600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:56425000-56431600	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr12:56425200-56427000	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr12:56425200-56429000	Strong transcription	Liver	Liver
44	chr12:56425200-56430000	Strong transcription	Adipose Nuclei	Adipose
45	chr12:56425200-56430600	Strong transcription	Primary hematopoietic stem cells	blood
46	chr12:56425200-56430800	Strong transcription	Left Ventricle	heart
47	chr12:56425200-56431400	Strong transcription	Brain Angular Gyrus	brain
48	chr12:56425200-56432800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:56425400-56426600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
50	chr12:56425400-56430000	Strong transcription	Fetal Brain Male	brain

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