Variant report

Variant	rs2541129
Chromosome Location	chr12:11816125-11816126
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:11815851..11817515-chr12:11821164..11823181,2	MCF-7	breast:
2	chr12:11814350..11816547-chr12:11823249..11825105,2	K562	blood:
3	chr12:11814416..11816234-chr12:11817623..11820133,2	MCF-7	breast:
4	chr12:11812795..11814731-chr12:11815428..11817529,2	K562	blood:
5	chr12:11801381..11803825-chr12:11814827..11819033,3	K562	blood:

Variant related genes	Relation type
ENSG00000139083	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10491985	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes]
rs10772496	1.00[CEU][hapmap]
rs11054413	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12578238	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1861482	0.82[CHB][hapmap];0.96[CHD][hapmap]
rs205542	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes]
rs205545	1.00[ASW][hapmap]
rs2111048	0.90[CHB][hapmap];0.96[CHD][hapmap]
rs2111049	0.82[CHB][hapmap];0.96[CHD][hapmap]
rs2111050	0.85[AFR][1000 genomes]
rs2277394	1.00[CEU][hapmap]
rs2416881	1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[EUR][1000 genomes]
rs2466582	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2541113	0.90[CHB][hapmap];0.96[CHD][hapmap]
rs2541116	0.87[AFR][1000 genomes]
rs2541121	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs2541122	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2541124	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2541126	0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs2541127	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2541128	0.82[CHB][hapmap];0.96[CHD][hapmap]
rs2724590	0.82[CHB][hapmap];0.96[CHD][hapmap]
rs2724592	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs2724605	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2724608	0.86[EUR][1000 genomes]
rs2724626	0.82[CHB][hapmap]
rs2724649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2856303	0.90[CHB][hapmap];1.00[CHD][hapmap]
rs2856308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2856309	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2856310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2856311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2856313	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs2856316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2908839	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3020922	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4503633	0.86[EUR][1000 genomes]
rs74062381	1.00[EUR][1000 genomes]
rs74062383	0.86[EUR][1000 genomes]
rs759484	1.00[ASW][hapmap];0.84[MKK][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs759485	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7963730	1.00[CEU][hapmap]
rs918074	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs928949	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs956753	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap]
rs9971751	0.86[EUR][1000 genomes]

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	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11806200-11816600	Weak transcription	Hela-S3	cervix
2	chr12:11806600-11819200	Weak transcription	NHLF	lung
3	chr12:11807800-11824200	Genic enhancers	Fetal Thymus	thymus
4	chr12:11808600-11816400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr12:11808600-11818800	Genic enhancers	Primary hematopoietic stem cells	blood
6	chr12:11809000-11820600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:11809200-11816600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:11810000-11816200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr12:11810800-11818600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:11811000-11817000	Weak transcription	Fetal Kidney	kidney
11	chr12:11812000-11825400	Weak transcription	HUVEC	blood vessel
12	chr12:11812200-11818200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:11812200-11819000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:11812200-11832600	Weak transcription	A549	lung
15	chr12:11812200-11837400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr12:11812400-11819400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:11812400-11830800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:11812800-11821400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:11812800-11825400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:11813000-11818800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:11813200-11822400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:11813400-11816200	Strong transcription	Primary B cells from cord blood	blood
23	chr12:11813400-11816600	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr12:11813400-11820800	Enhancers	Left Ventricle	heart
25	chr12:11813600-11816400	Enhancers	Pancreas	Pancrea
26	chr12:11813600-11816600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:11813800-11817200	Enhancers	Colon Smooth Muscle	Colon
28	chr12:11813800-11817200	Enhancers	Right Atrium	heart
29	chr12:11814000-11816400	Enhancers	Esophagus	oesophagus
30	chr12:11814000-11816400	Enhancers	Gastric	stomach
31	chr12:11814000-11816600	Genic enhancers	Monocytes-CD14+_RO01746	blood
32	chr12:11814000-11817000	Enhancers	Rectal Smooth Muscle	rectum
33	chr12:11814200-11816400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:11814200-11816600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr12:11814200-11819000	Enhancers	Psoas Muscle	Psoas
36	chr12:11814400-11816200	Genic enhancers	Primary T cells from cord blood	blood
37	chr12:11814400-11816200	Genic enhancers	GM12878-XiMat	blood
38	chr12:11814400-11816600	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr12:11814400-11816600	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr12:11814400-11827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:11814600-11817400	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr12:11814600-11817600	Enhancers	Brain Substantia Nigra	brain
43	chr12:11814800-11816200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr12:11814800-11816400	Enhancers	Placenta	Placenta
45	chr12:11814800-11816800	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr12:11814800-11818200	Enhancers	Right Ventricle	heart
47	chr12:11814800-11818800	Strong transcription	Dnd41	blood
48	chr12:11814800-11826600	Weak transcription	Osteobl	bone
49	chr12:11814800-11829000	Weak transcription	Fetal Intestine Large	intestine
50	chr12:11815000-11816200	Weak transcription	Fetal Lung	lung

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