Variant report

Variant	rs6539162
Chromosome Location	chr12:104993579-104993580
allele	C/G
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104989262..104996194-chr12:104996249..105001190,9	K562	blood:
2	chr12:104877368..104879686-chr12:104993577..104996445,2	K562	blood:
3	chr12:104612288..104614036-chr12:104992703..104994366,2	K562	blood:
4	chr12:104982094..104985364-chr12:104993375..104995916,3	K562	blood:
5	chr12:104972360..104974228-chr12:104993153..104995574,2	K562	blood:
6	chr12:104849537..104851746-chr12:104993133..104995446,2	K562	blood:
7	chr12:104990754..104993750-chr12:104994386..104996312,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000171310	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10746004	0.88[EUR][1000 genomes]
rs10778342	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704896	0.81[EUR][1000 genomes]
rs2162661	0.96[EUR][1000 genomes]
rs2888827	0.92[EUR][1000 genomes]
rs3812796	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6539163	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539164	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316145	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972130	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1035364	chr12:104948307-105003705	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104976800-104996800	Weak transcription	Primary T cells from cord blood	blood
2	chr12:104980200-104997600	Weak transcription	Esophagus	oesophagus
3	chr12:104982600-104994800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:104982800-104995400	Weak transcription	Thymus	Thymus
5	chr12:104983200-104996800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr12:104983200-104997800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:104985000-104996400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:104987800-104997800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:104988000-104997000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:104988000-104997200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr12:104988600-104994800	Enhancers	Primary B cells from peripheral blood	blood
12	chr12:104988800-104995600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr12:104988800-104995600	Enhancers	GM12878-XiMat	blood
14	chr12:104989200-104997800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:104989400-104995400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr12:104989400-104995800	Enhancers	Placenta	Placenta
17	chr12:104989400-104997800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr12:104989400-105030600	Strong transcription	Dnd41	blood
19	chr12:104990000-104994200	Enhancers	Fetal Muscle Leg	muscle
20	chr12:104990000-104994600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr12:104990000-104995200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr12:104990000-104995400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:104990200-104995800	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr12:104990400-104994600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:104990400-104995200	Enhancers	Primary hematopoietic stem cells	blood
26	chr12:104990600-104993600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:104990600-104993600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:104990600-104994200	Enhancers	Lung	lung
29	chr12:104990600-104995600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:104990800-104997600	Weak transcription	Brain Angular Gyrus	brain
31	chr12:104991000-104994800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:104991000-104994800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr12:104991000-104995200	Weak transcription	NHEK	skin
34	chr12:104991000-104996000	Weak transcription	Fetal Brain Female	brain
35	chr12:104991000-104997600	Weak transcription	Left Ventricle	heart
36	chr12:104991000-104997600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr12:104991000-104997800	Weak transcription	Aorta	Aorta
38	chr12:104991200-104995600	Weak transcription	Primary B cells from cord blood	blood
39	chr12:104991400-104994800	Weak transcription	Fetal Stomach	stomach
40	chr12:104991400-104995200	Weak transcription	HMEC	breast
41	chr12:104991400-104997200	Weak transcription	Colon Smooth Muscle	Colon
42	chr12:104991400-104997600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:104991600-104994600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:104991600-104995400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:104991600-104995400	Weak transcription	HSMM	muscle
46	chr12:104991600-104995600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr12:104991600-104996200	Weak transcription	Fetal Brain Male	brain
48	chr12:104991600-104996600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:104991600-104998000	Weak transcription	Fetal Kidney	kidney
50	chr12:104991800-104994800	Weak transcription	NHLF	lung

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