Variant report

Variant	rs6539163
Chromosome Location	chr12:104996237-104996238
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104995437..104998034-chr12:105005195..105009191,4	K562	blood:
2	chr12:104877368..104879686-chr12:104993577..104996445,2	K562	blood:
3	chr12:104995476..104999568-chr12:105000294..105003603,4	MCF-7	breast:
4	chr12:104877368..104879475-chr12:104994945..104997533,2	K562	blood:
5	chr12:104995437..104998034-chr12:105002964..105009191,6	K562	blood:
6	chr12:104990754..104993750-chr12:104994386..104996312,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10746004	1.00[CEU][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs10778342	0.93[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162661	1.00[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs2888827	0.94[EUR][1000 genomes]
rs3812796	0.94[CEU][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6539162	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539164	1.00[CEU][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316145	1.00[CEU][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972130	0.91[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:105 , 50 per page) page: 1 2 3

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	chr12:104983200-104996800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr12:104983200-104997800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:104985000-104996400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:104987800-104997800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:104988000-104997000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:104988000-104997200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr12:104989200-104997800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:104989400-104997800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr12:104989400-105030600	Strong transcription	Dnd41	blood
12	chr12:104990800-104997600	Weak transcription	Brain Angular Gyrus	brain
13	chr12:104991000-104997600	Weak transcription	Left Ventricle	heart
14	chr12:104991000-104997600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:104991000-104997800	Weak transcription	Aorta	Aorta
16	chr12:104991400-104997200	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:104991400-104997600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:104991600-104996600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:104991600-104998000	Weak transcription	Fetal Kidney	kidney
20	chr12:104991800-104997600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:104992000-104996600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:104992200-104997400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr12:104992400-104997600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:104992600-104996400	Weak transcription	NH-A	brain
25	chr12:104992800-104997200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:104992800-104997400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:104992800-104997800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:104993000-104997600	Weak transcription	Right Ventricle	heart
29	chr12:104993200-104997600	Weak transcription	Small Intestine	intestine
30	chr12:104993200-104999400	Weak transcription	Brain Germinal Matrix	brain
31	chr12:104993200-105006200	Weak transcription	Fetal Heart	heart
32	chr12:104993200-105012600	Weak transcription	Gastric	stomach
33	chr12:104993400-104999600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:104993600-104997600	Enhancers	NHDF-Ad	bronchial
35	chr12:104993800-104996800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:104993800-104997600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr12:104993800-104998000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:104994000-104996800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:104994200-104996600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr12:104994200-104997800	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:104994800-104997400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr12:104994800-104997600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:104995000-104997200	Genic enhancers	Fetal Thymus	thymus
44	chr12:104995000-104997400	Weak transcription	Adipose Nuclei	Adipose
45	chr12:104995200-104996400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:104995200-104996400	Enhancers	Lung	lung
47	chr12:104995200-104996800	Genic enhancers	Primary hematopoietic stem cells	blood
48	chr12:104995200-104997200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr12:104995200-104997600	Enhancers	HUVEC	blood vessel
50	chr12:104995200-104997800	Enhancers	NHEK	skin

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