Variant report

Variant	rs2126140
Chromosome Location	chr3:121145268-121145269
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121143314..121145833-chr3:121149976..121152815,2	MCF-7	breast:

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10451895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10934551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11705939	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11707252	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11707354	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11708438	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11709726	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11711667	0.85[EUR][1000 genomes]
rs11713643	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11715085	0.85[ASN][1000 genomes]
rs11718918	0.83[EUR][1000 genomes]
rs12233510	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12488196	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs12496163	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12632308	0.85[EUR][1000 genomes]
rs12634017	0.81[ASN][1000 genomes]
rs12635218	0.84[EUR][1000 genomes]
rs13059229	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs13065220	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs13076688	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13077305	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs13080007	0.86[EUR][1000 genomes]
rs13081748	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13082118	1.00[JPT][hapmap]
rs13085365	0.81[EUR][1000 genomes]
rs13086811	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13095841	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097659	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1381057	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1381058	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1381059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1986730	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1987097	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1987098	0.95[ASN][1000 genomes]
rs2030531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2126139	0.98[ASN][1000 genomes]
rs2127024	0.95[ASN][1000 genomes]
rs2169300	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2331921	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28406368	0.80[EUR][1000 genomes]
rs3218649	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs3732405	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3732406	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs3772122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs3806614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3843345	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3911713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4107754	0.91[ASN][1000 genomes]
rs4346498	0.91[ASN][1000 genomes]
rs4555467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4676677	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4676722	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs502643	1.00[JPT][hapmap]
rs541818	0.81[ASN][1000 genomes]
rs587553	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs61796944	0.93[ASN][1000 genomes]
rs6438625	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6438626	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6438630	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6438631	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6438633	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6765310	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6769377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6778684	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6782025	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6782033	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6787048	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6793029	0.91[ASN][1000 genomes]
rs6793252	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6796068	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6797376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6798699	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6806191	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs693403	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs702019	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7609781	0.95[ASN][1000 genomes]
rs7612018	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7613752	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7614639	0.82[EUR][1000 genomes]
rs7615529	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs7618570	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7621376	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7622867	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7622881	1.00[JPT][hapmap]
rs7622897	0.84[EUR][1000 genomes]
rs7627978	0.95[ASN][1000 genomes]
rs7632907	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7633930	0.88[JPT][hapmap]
rs7634611	0.95[ASN][1000 genomes]
rs7644928	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7645027	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7645544	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7645849	0.95[ASN][1000 genomes]
rs7645869	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7650439	0.95[ASN][1000 genomes]
rs7650658	0.95[ASN][1000 genomes]
rs9849118	0.95[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	nsv998555	chr3:120700604-121348015	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv521397	chr3:120970900-121192350	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv829702	chr3:121045793-121227975	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv591398	chr3:121046468-121154193	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv591399	chr3:121046468-121160369	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv591400	chr3:121070299-121339354	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv591401	chr3:121094592-121160369	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121129200-121148800	Weak transcription	GM12878-XiMat	blood
2	chr3:121134200-121152600	Weak transcription	Hela-S3	cervix
3	chr3:121134600-121146400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:121135800-121148600	Weak transcription	Thymus	Thymus
5	chr3:121135800-121149000	Weak transcription	A549	lung
6	chr3:121137600-121145800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:121137800-121148800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:121139000-121145800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:121139200-121150600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:121139200-121186000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:121139400-121147400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:121140200-121149000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:121140600-121147000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:121140600-121150800	Weak transcription	HSMM	muscle
15	chr3:121140600-121170800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:121140800-121148400	Weak transcription	Fetal Thymus	thymus
17	chr3:121140800-121149000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:121140800-121150800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:121140800-121151400	Weak transcription	HepG2	liver
20	chr3:121141000-121148800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:121141200-121186000	Weak transcription	NHEK	skin
22	chr3:121141600-121147000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:121141600-121148600	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr3:121141800-121146800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:121141800-121147200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:121142000-121145400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:121142200-121161600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:121142600-121151000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:121143000-121147400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:121143000-121148200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:121143200-121145800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:121143200-121147400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:121143200-121148600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:121143200-121150800	Weak transcription	NHLF	lung
35	chr3:121143400-121150800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:121143600-121160000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr3:121144200-121148600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:121144400-121148600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:121144600-121150600	Strong transcription	Dnd41	blood
40	chr3:121144800-121147200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr3:121144800-121150800	Weak transcription	HUVEC	blood vessel
42	chr3:121145200-121150600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:121145200-121160200	Strong transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links