Variant report

Variant	rs3812796
Chromosome Location	chr12:104995459-104995460
allele	A/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104995437..104998034-chr12:105005195..105009191,4	K562	blood:
2	chr12:104989262..104996194-chr12:104996249..105001190,9	K562	blood:
3	chr12:104877368..104879686-chr12:104993577..104996445,2	K562	blood:
4	chr12:104994126..104996076-chr12:105024085..105026478,2	K562	blood:
5	chr12:104982094..104985364-chr12:104993375..104995916,3	K562	blood:
6	chr12:104877368..104879475-chr12:104994945..104997533,2	K562	blood:
7	chr12:104972360..104974228-chr12:104993153..104995574,2	K562	blood:
8	chr12:104969237..104970979-chr12:104994283..104996065,2	MCF-7	breast:
9	chr12:104995437..104998034-chr12:105002964..105009191,6	K562	blood:
10	chr12:104990754..104993750-chr12:104994386..104996312,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000171310	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10746004	0.94[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs10778342	0.94[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112131	0.91[CHB][hapmap];0.94[ASN][1000 genomes]
rs11836281	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs17035941	0.90[CHB][hapmap];0.92[ASN][1000 genomes]
rs17035961	0.91[CHB][hapmap];0.94[ASN][1000 genomes]
rs2162661	0.94[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs2888827	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6539162	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6539163	0.94[CEU][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6539164	0.94[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs7316145	0.94[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs7972130	0.90[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3812796	CRY1	cis	parietal	SCAN
rs3812796	UTP20	cis	parietal	SCAN

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	chr12:104988800-104995600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr12:104988800-104995600	Enhancers	GM12878-XiMat	blood
11	chr12:104989200-104997800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:104989400-104995800	Enhancers	Placenta	Placenta
13	chr12:104989400-104997800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr12:104989400-105030600	Strong transcription	Dnd41	blood
15	chr12:104990200-104995800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr12:104990600-104995600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:104990800-104997600	Weak transcription	Brain Angular Gyrus	brain
18	chr12:104991000-104996000	Weak transcription	Fetal Brain Female	brain
19	chr12:104991000-104997600	Weak transcription	Left Ventricle	heart
20	chr12:104991000-104997600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:104991000-104997800	Weak transcription	Aorta	Aorta
22	chr12:104991200-104995600	Weak transcription	Primary B cells from cord blood	blood
23	chr12:104991400-104997200	Weak transcription	Colon Smooth Muscle	Colon
24	chr12:104991400-104997600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:104991600-104995600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:104991600-104996200	Weak transcription	Fetal Brain Male	brain
27	chr12:104991600-104996600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:104991600-104998000	Weak transcription	Fetal Kidney	kidney
29	chr12:104991800-104996200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:104991800-104997600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr12:104992000-104996600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:104992200-104995600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:104992200-104997400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr12:104992400-104995600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:104992400-104997600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:104992600-104996400	Weak transcription	NH-A	brain
37	chr12:104992800-104995800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:104992800-104997200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr12:104992800-104997400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr12:104992800-104997800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:104993000-104997600	Weak transcription	Right Ventricle	heart
42	chr12:104993200-104997600	Weak transcription	Small Intestine	intestine
43	chr12:104993200-104999400	Weak transcription	Brain Germinal Matrix	brain
44	chr12:104993200-105006200	Weak transcription	Fetal Heart	heart
45	chr12:104993200-105012600	Weak transcription	Gastric	stomach
46	chr12:104993400-104995600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:104993400-104999600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:104993600-104997600	Enhancers	NHDF-Ad	bronchial
49	chr12:104993800-104996800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:104993800-104997600	Weak transcription	Rectal Mucosa Donor 29	rectum

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