Variant report

Variant	rs3129990
Chromosome Location	chr6:30814543-30814544
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30718958..30721409-chr6:30812435..30814738,2	MCF-7	breast:
2	chr6:30796590..30799414-chr6:30814456..30816508,2	K562	blood:
3	chr6:30814424..30817937-chr6:30849019..30852528,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204580	Chromatin interaction
ENSG00000214894	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs2394449	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2394450	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2394451	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2517582	0.83[ASN][1000 genomes]
rs2535338	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3094109	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3094720	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3095342	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3095343	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3095344	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3095346	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3095348	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3095349	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3095350	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3095351	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3095352	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3095354	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3129993	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130649	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130650	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3130651	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130652	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3130653	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130655	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3130656	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130786	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3130787	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130789	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3130791	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130792	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130793	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130794	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130795	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130796	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3131027	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3131030	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3131031	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3131066	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132573	0.86[EUR][1000 genomes]
rs3132574	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3132575	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3132576	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3132578	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9262251	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
5	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
7	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30806800-30816200	Enhancers	Placenta	Placenta
2	chr6:30812000-30814800	Weak transcription	Fetal Kidney	kidney
3	chr6:30812000-30815400	Enhancers	Thymus	Thymus
4	chr6:30812000-30816200	Enhancers	Fetal Thymus	thymus
5	chr6:30812200-30815000	Weak transcription	Adipose Nuclei	Adipose
6	chr6:30812400-30814600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr6:30812400-30814800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:30812400-30815200	Weak transcription	HMEC	breast
9	chr6:30812400-30817000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:30812400-30822600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:30812600-30814800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:30812600-30814800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:30812600-30814800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:30812600-30814800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:30812600-30814800	Weak transcription	NHEK	skin
16	chr6:30812600-30815000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:30812600-30815000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:30812600-30815200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:30812600-30815200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:30812600-30815200	Weak transcription	Esophagus	oesophagus
21	chr6:30812600-30815200	Weak transcription	Fetal Lung	lung
22	chr6:30812600-30815400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:30812600-30820600	Weak transcription	Right Atrium	heart
24	chr6:30812800-30817000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:30813200-30814800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr6:30813200-30815000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr6:30813400-30814600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:30813600-30814600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:30813600-30815000	Weak transcription	K562	blood
30	chr6:30813600-30815200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:30813600-30816000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:30813800-30814600	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr6:30813800-30814800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:30813800-30814800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:30813800-30815000	Weak transcription	Fetal Heart	heart
36	chr6:30814000-30814600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr6:30814000-30814800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:30814000-30814800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:30814000-30815200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:30814000-30815400	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr6:30814000-30817000	Weak transcription	Fetal Intestine Small	intestine
42	chr6:30814200-30814800	Enhancers	H1 Cell Line	embryonic stem cell
43	chr6:30814200-30814800	Weak transcription	Dnd41	blood
44	chr6:30814400-30815800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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