Variant report

Variant	rs7962283
Chromosome Location	chr12:39834622-39834623
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:39707343..39709850-chr12:39833796..39835957,2	K562	blood:
2	chr12:39807290..39809220-chr12:39833749..39836763,3	K562	blood:
3	chr12:39815681..39818065-chr12:39831801..39835369,3	K562	blood:
4	chr12:39834094..39836682-chr12:39930769..39933635,3	K562	blood:
5	chr12:39708256..39710912-chr12:39833762..39835679,2	MCF-7	breast:
6	chr12:39743944..39745971-chr12:39833401..39836053,2	K562	blood:
7	chr12:39806434..39808790-chr12:39833185..39835249,2	K562	blood:
8	chr12:39759047..39762172-chr12:39834495..39838400,6	MCF-7	breast:
9	chr12:39801655..39803705-chr12:39833812..39835448,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000139116	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10876886	0.96[CEU][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs10876972	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876989	0.81[EUR][1000 genomes]
rs10877100	0.83[EUR][1000 genomes]
rs11171675	0.82[CEU][hapmap]
rs11171720	0.83[CEU][hapmap]
rs11171789	0.83[CEU][hapmap]
rs11171891	0.83[CEU][hapmap]
rs11171901	0.86[CEU][hapmap]
rs11171923	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs11171938	0.84[CEU][hapmap]
rs11172081	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11172108	0.96[CEU][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172120	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172174	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172183	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172235	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172264	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11172282	0.84[CEU][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172293	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172357	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11172386	0.85[EUR][1000 genomes]
rs11172392	0.84[EUR][1000 genomes]
rs11172492	1.00[CEU][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11172493	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11172526	0.83[EUR][1000 genomes]
rs11172592	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs11172661	0.87[CEU][hapmap];0.92[YRI][hapmap]
rs11830643	0.95[CEU][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs12228767	0.95[CEU][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs12230604	0.87[CEU][hapmap]
rs12424345	1.00[CEU][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs1512936	0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs1567739	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs1828653	0.87[CEU][hapmap]
rs2388320	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs3736466	0.83[CEU][hapmap]
rs4284427	0.91[CEU][hapmap]
rs4320988	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4390378	0.86[EUR][1000 genomes]
rs4492858	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4500523	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs4564382	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58240943	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58613501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59695906	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60900225	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6581187	0.83[EUR][1000 genomes]
rs7133376	0.92[YRI][hapmap]
rs7137143	0.83[CEU][hapmap]
rs73094410	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316073	0.92[CEU][hapmap]
rs7964447	0.96[CEU][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs7965222	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7968837	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs7974928	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs7979444	0.87[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39821400-39835600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:39825200-39835600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:39829600-39835800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:39830000-39835400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:39830600-39834800	Enhancers	Fetal Heart	heart
6	chr12:39832200-39835600	Enhancers	Liver	Liver
7	chr12:39833000-39835200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:39833600-39835000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr12:39833600-39836400	Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr12:39833800-39835200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:39833800-39835600	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr12:39833800-39836200	Active TSS	Brain Germinal Matrix	brain
13	chr12:39833800-39837800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:39834000-39834800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:39834000-39834800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr12:39834000-39834800	Enhancers	Pancreas	Pancrea
17	chr12:39834000-39835400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr12:39834000-39835400	Flanking Active TSS	A549	lung
19	chr12:39834000-39835400	Flanking Active TSS	K562	blood
20	chr12:39834000-39835600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:39834000-39837600	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr12:39834000-39838000	Active TSS	Right Atrium	heart
23	chr12:39834200-39835000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr12:39834200-39835200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr12:39834200-39835400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr12:39834200-39838000	Active TSS	Brain Angular Gyrus	brain
27	chr12:39834400-39834800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:39834400-39834800	Weak transcription	Fetal Intestine Small	intestine
29	chr12:39834400-39834800	Enhancers	Psoas Muscle	Psoas
30	chr12:39834400-39834800	Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr12:39834400-39834800	Flanking Active TSS	GM12878-XiMat	blood
32	chr12:39834400-39835000	Flanking Active TSS	Fetal Brain Male	brain
33	chr12:39834400-39835000	Enhancers	HMEC	breast
34	chr12:39834400-39835200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:39834400-39835200	Enhancers	Brain Hippocampus Middle	brain
36	chr12:39834400-39835400	Flanking Active TSS	HepG2	liver
37	chr12:39834400-39837400	Active TSS	Fetal Brain Female	brain
38	chr12:39834400-39837800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:39834400-39837800	Active TSS	Right Ventricle	heart
40	chr12:39834600-39834800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr12:39834600-39834800	Enhancers	Primary T cells fromperipheralblood	blood
42	chr12:39834600-39834800	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr12:39834600-39834800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:39834600-39834800	Enhancers	Placenta	Placenta
45	chr12:39834600-39834800	Flanking Active TSS	Left Ventricle	heart
46	chr12:39834600-39834800	Enhancers	Lung	lung
47	chr12:39834600-39834800	Flanking Active TSS	NHEK	skin
48	chr12:39834600-39835000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr12:39834600-39835000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:39834600-39835000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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