Variant report

Variant	rs7973255
Chromosome Location	chr12:10752344-10752345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10752173..10753763-chr12:10760040..10762966,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAGOHB-1	chr12:10752121-10752434	XLOC_010017
2	lnc-MAGOHB-1	chr12:10752121-10752434	NONHSAT026890
3	lnc-MAGOHB-1	chr12:10752121-10752434	NR_028045

Variant related genes	Relation type
ENSG00000111196	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1003029	0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11053888	1.00[CHD][hapmap]
rs1124164	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829102	0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11830025	0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834676	1.00[CHD][hapmap];0.94[MKK][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304656	1.00[CHD][hapmap]
rs12370025	1.00[ASW][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16921917	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16922006	1.00[CHD][hapmap];0.91[LWK][hapmap];1.00[ASN][1000 genomes]
rs16922007	1.00[ASN][1000 genomes]
rs16922807	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4280083	1.00[ASN][1000 genomes]
rs4763206	1.00[ASW][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4763207	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4763560	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4763561	1.00[ASW][hapmap];1.00[CHD][hapmap];0.96[LWK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59582425	1.00[ASN][1000 genomes]
rs7297513	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7313116	0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7315723	1.00[EUR][1000 genomes]
rs73256073	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73256078	1.00[ASN][1000 genomes]
rs73256092	1.00[ASN][1000 genomes]
rs73257957	1.00[ASN][1000 genomes]
rs73257964	1.00[ASN][1000 genomes]
rs73257985	1.00[ASN][1000 genomes]
rs73257988	1.00[ASN][1000 genomes]
rs73262002	1.00[ASN][1000 genomes]
rs7952776	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7953309	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7955193	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7955402	1.00[ASN][1000 genomes]
rs7958146	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958230	1.00[ASN][1000 genomes]
rs7958735	1.00[ASN][1000 genomes]
rs7964590	0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7969057	1.00[ASN][1000 genomes]
rs7976533	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039120	chr12:10675930-10755446	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv832329	chr12:10677094-10845946	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10725600-10765000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:10725800-10753400	Weak transcription	Osteobl	bone
3	chr12:10725800-10761400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:10726400-10759800	Weak transcription	NHLF	lung
5	chr12:10726800-10756600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:10730000-10762000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:10730600-10764800	Weak transcription	Lung	lung
8	chr12:10730800-10758400	Weak transcription	NHEK	skin
9	chr12:10731200-10756400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr12:10731400-10753200	Weak transcription	Primary B cells from cord blood	blood
11	chr12:10731600-10760800	Weak transcription	Fetal Brain Female	brain
12	chr12:10732000-10759600	Weak transcription	Fetal Intestine Large	intestine
13	chr12:10732000-10759800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:10732200-10759600	Weak transcription	Left Ventricle	heart
15	chr12:10732200-10761400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:10732200-10764800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:10732400-10759600	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:10732400-10764200	Weak transcription	Pancreas	Pancrea
19	chr12:10732600-10759600	Weak transcription	HMEC	breast
20	chr12:10732800-10759600	Weak transcription	Brain Hippocampus Middle	brain
21	chr12:10733400-10759600	Weak transcription	HUVEC	blood vessel
22	chr12:10733600-10759800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:10733800-10753400	Weak transcription	Dnd41	blood
24	chr12:10733800-10760000	Weak transcription	Fetal Brain Male	brain
25	chr12:10734000-10753200	Weak transcription	Liver	Liver
26	chr12:10734000-10759400	Weak transcription	Fetal Lung	lung
27	chr12:10734000-10764000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:10734000-10764600	Weak transcription	Thymus	Thymus
29	chr12:10734200-10755200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:10734200-10757400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr12:10734200-10759400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr12:10734200-10759400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:10734200-10759400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr12:10734200-10759600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr12:10734200-10762200	Weak transcription	Fetal Muscle Leg	muscle
36	chr12:10734200-10764000	Weak transcription	Fetal Stomach	stomach
37	chr12:10734400-10753600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr12:10734400-10754400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr12:10734400-10754600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr12:10734400-10756600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:10734400-10764600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:10735200-10753200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:10735200-10759600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:10735200-10764600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:10735400-10764000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr12:10736400-10758600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:10736600-10756600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:10738800-10764000	Weak transcription	Fetal Intestine Small	intestine
49	chr12:10739400-10761400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:10741600-10756600	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links