Variant report

Variant	rs1222141
Chromosome Location	chr1:223926406-223926407
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223891443..223896975-chr1:223925207..223929791,6	MCF-7	breast:
2	chr1:223924785..223927259-chr1:223936900..223938830,2	K562	blood:
3	chr1:223906267..223909049-chr1:223925924..223927616,2	MCF-7	breast:
4	chr1:223926311..223927941-chr1:223933092..223935068,2	K562	blood:
5	chr1:223925259..223927259-chr1:223937310..223938830,2	K562	blood:
6	chr1:223924368..223926769-chr1:223968941..223970904,2	K562	blood:
7	chr1:223898969..223903164-chr1:223924094..223928992,8	MCF-7	breast:
8	chr1:223918635..223922245-chr1:223925850..223929641,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10465524	0.85[CEU][hapmap]
rs10495215	0.85[CEU][hapmap]
rs10495216	0.85[CEU][hapmap]
rs10495217	0.85[CEU][hapmap]
rs10503144	0.85[CEU][hapmap]
rs10915702	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10915707	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10915715	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916634	0.87[CEU][hapmap]
rs10916646	0.87[CEU][hapmap]
rs1153965	0.85[EUR][1000 genomes]
rs12059128	0.81[EUR][1000 genomes]
rs12059770	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12060361	0.81[EUR][1000 genomes]
rs12066704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12066829	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12066831	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12069561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12070057	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12070364	0.87[CEU][hapmap]
rs12080250	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs12088254	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs12091841	0.81[EUR][1000 genomes]
rs1222134	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1222138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1222140	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222142	0.91[EUR][1000 genomes]
rs12562109	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12563291	0.89[EUR][1000 genomes]
rs12563477	0.83[EUR][1000 genomes]
rs12563637	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs12563713	0.87[EUR][1000 genomes]
rs12565967	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12566817	0.85[CEU][hapmap]
rs1419305	0.87[CEU][hapmap]
rs1629836	0.82[CEU][hapmap]
rs16842162	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs16842229	0.81[EUR][1000 genomes]
rs16842257	0.85[CEU][hapmap]
rs16842326	0.85[CEU][hapmap]
rs17557288	0.85[CEU][hapmap]
rs17557525	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs17557623	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs17597	0.89[EUR][1000 genomes]
rs17598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17600	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1779658	0.87[CEU][hapmap]
rs1892077	0.87[CEU][hapmap]
rs2186006	0.87[CEU][hapmap]
rs28370026	0.84[EUR][1000 genomes]
rs28370031	0.84[EUR][1000 genomes]
rs28370032	0.84[EUR][1000 genomes]
rs28370043	0.85[EUR][1000 genomes]
rs28370069	0.85[EUR][1000 genomes]
rs28370073	0.81[EUR][1000 genomes]
rs28370074	0.81[EUR][1000 genomes]
rs28370088	0.81[EUR][1000 genomes]
rs28370170	0.83[EUR][1000 genomes]
rs34683843	0.81[EUR][1000 genomes]
rs3738373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3738374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3738375	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3767716	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3767717	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3767718	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3885657	0.81[EUR][1000 genomes]
rs59248553	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59275322	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61823979	0.81[EUR][1000 genomes]
rs61824003	0.83[EUR][1000 genomes]
rs61824005	0.82[EUR][1000 genomes]
rs61824008	0.81[EUR][1000 genomes]
rs6604724	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs6665485	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6669046	0.87[CEU][hapmap]
rs6669080	1.00[CEU][hapmap]
rs6671245	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs6674541	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6674846	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6678365	0.85[CEU][hapmap]
rs6682412	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6682964	0.81[EUR][1000 genomes]
rs6683052	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs6685475	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs6685557	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs6691315	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs6693372	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs6693884	0.84[EUR][1000 genomes]
rs6694960	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs6696053	0.85[CEU][hapmap]
rs6700366	0.85[CEU][hapmap]
rs7331	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs7412088	0.87[CEU][hapmap]
rs751609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7530328	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7533551	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7535882	0.85[CEU][hapmap]
rs7543197	0.87[CEU][hapmap]
rs7547642	0.87[CEU][hapmap]
rs7549063	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs7555226	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7555491	0.87[CEU][hapmap]
rs898876	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs898877	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223915200-223930800	Weak transcription	Primary T cells from cord blood	blood
2	chr1:223915400-223927200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:223915400-223936200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:223915800-223931600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:223916600-223927000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:223916600-223932600	Weak transcription	Fetal Brain Female	brain
9	chr1:223919200-223935600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:223919200-223936200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr1:223919800-223931200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:223921200-223927800	Genic enhancers	A549	lung
13	chr1:223921200-223932800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:223921200-223936000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:223921400-223931400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:223921600-223932800	Weak transcription	Liver	Liver
17	chr1:223921600-223936600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:223921800-223933400	Weak transcription	Brain Angular Gyrus	brain
19	chr1:223921800-223935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:223921800-223936000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:223922200-223934600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:223922200-223935600	Weak transcription	Fetal Brain Male	brain
23	chr1:223922400-223926600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:223922400-223927400	Weak transcription	Small Intestine	intestine
25	chr1:223922400-223927800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:223922600-223927200	Weak transcription	Fetal Lung	lung
27	chr1:223922600-223927200	Weak transcription	K562	blood
28	chr1:223922600-223928000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:223922800-223927200	Weak transcription	Psoas Muscle	Psoas
30	chr1:223922800-223928600	Weak transcription	Fetal Thymus	thymus
31	chr1:223922800-223930600	Weak transcription	Spleen	Spleen
32	chr1:223922800-223930800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:223922800-223931600	Weak transcription	Brain Germinal Matrix	brain
34	chr1:223922800-223934800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:223923000-223926600	Weak transcription	Brain Substantia Nigra	brain
36	chr1:223923000-223927200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:223923000-223928600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:223923000-223931800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr1:223923200-223928000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:223923200-223928200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:223923400-223927400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:223923800-223929400	Genic enhancers	NHEK	skin
43	chr1:223924000-223926600	Genic enhancers	HSMM	muscle
44	chr1:223924200-223928000	Enhancers	Stomach Smooth Muscle	stomach
45	chr1:223924400-223928000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:223924800-223927200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:223924800-223927400	Genic enhancers	Fetal Intestine Small	intestine
48	chr1:223924800-223928400	Enhancers	Aorta	Aorta
49	chr1:223924800-223929800	Enhancers	Placenta Amnion	Placenta Amnion
50	chr1:223925200-223927200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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