Variant report

Variant	rs7299689
Chromosome Location	chr12:48201317-48201318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48173557..48179365-chr12:48198461..48203449,6	K562	blood:
2	chr12:48200516..48204856-chr12:48204984..48208825,6	K562	blood:
3	chr12:48200947..48203542-chr12:48208832..48210426,2	K562	blood:

Variant related genes	Relation type
ENSG00000268069	Chromatin interaction
ENSG00000061273	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11837686	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814620	1.00[ASN][1000 genomes]
rs12820931	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12828203	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12828577	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122326	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34248545	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34379708	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34785684	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35392237	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580638	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71462981	1.00[ASN][1000 genomes]
rs7303453	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971594	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980930	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
2	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
3	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
4	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
7	nsv899060	chr12:48180508-48231430	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	esv3693398	chr12:48186738-48215749	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv1048466	chr12:48195350-48262541	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv541488	chr12:48195350-48262541	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	esv999028	chr12:48199301-48209132	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48182000-48206400	Weak transcription	HepG2	liver
2	chr12:48182400-48202000	Weak transcription	Fetal Brain Male	brain
3	chr12:48183000-48204000	Weak transcription	Fetal Kidney	kidney
4	chr12:48190800-48201400	Genic enhancers	Fetal Thymus	thymus
5	chr12:48191400-48201400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:48191400-48202800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:48191600-48201600	Genic enhancers	Thymus	Thymus
8	chr12:48192400-48201600	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr12:48192400-48203200	Enhancers	Right Atrium	heart
10	chr12:48192600-48201400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr12:48193400-48203000	Enhancers	Fetal Heart	heart
12	chr12:48193400-48205000	Weak transcription	Brain Germinal Matrix	brain
13	chr12:48193600-48201400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:48193800-48201600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr12:48194400-48201400	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr12:48195200-48201600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:48196200-48201600	Enhancers	Primary hematopoietic stem cells	blood
18	chr12:48196800-48201600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:48196800-48201600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:48197000-48201400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:48197000-48201800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:48197200-48201800	Enhancers	Rectal Smooth Muscle	rectum
23	chr12:48197200-48203400	Enhancers	Psoas Muscle	Psoas
24	chr12:48197800-48202600	Weak transcription	Liver	Liver
25	chr12:48198000-48203200	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr12:48198200-48201400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:48198200-48203400	Enhancers	Right Ventricle	heart
28	chr12:48198400-48201400	Weak transcription	HSMMtube	muscle
29	chr12:48198600-48201600	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr12:48198800-48201400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:48198800-48201600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:48199200-48203400	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr12:48199400-48201400	Weak transcription	HMEC	breast
34	chr12:48199400-48201800	Enhancers	Adipose Nuclei	Adipose
35	chr12:48199400-48201800	Enhancers	Duodenum Mucosa	Duodenum
36	chr12:48199400-48203400	Enhancers	Left Ventricle	heart
37	chr12:48199400-48206400	Weak transcription	Fetal Brain Female	brain
38	chr12:48199600-48203200	Enhancers	Stomach Mucosa	stomach
39	chr12:48199600-48203400	Enhancers	NHDF-Ad	bronchial
40	chr12:48199800-48202800	Genic enhancers	Fetal Intestine Small	intestine
41	chr12:48199800-48204000	Weak transcription	Aorta	Aorta
42	chr12:48199800-48206800	Enhancers	Spleen	Spleen
43	chr12:48200000-48201400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:48200000-48201400	Weak transcription	Fetal Lung	lung
45	chr12:48200000-48201600	Enhancers	Primary B cells from peripheral blood	blood
46	chr12:48200000-48201600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:48200000-48202800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:48200000-48203400	Enhancers	Gastric	stomach
49	chr12:48200000-48203600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr12:48200000-48204800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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