Variant report

Variant	rs3768569
Chromosome Location	chr1:171157708-171157709
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171049785..171051089-chr1:171157506..171158409,9	MCF-7	breast:
2	chr1:170936285..170936841-chr1:171157519..171158468,2	MCF-7	breast:
3	chr1:171157094..171159925-chr1:171161242..171162761,2	K562	blood:
4	chr1:171050091..171050825-chr1:171157560..171158443,3	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10798252	0.81[ASN][1000 genomes]
rs10798263	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10912537	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10912538	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10912552	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11806072	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11810116	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12078953	0.96[JPT][hapmap]
rs12080576	0.94[JPT][hapmap]
rs12085225	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12092242	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12566823	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12567059	0.92[ASN][1000 genomes]
rs12567358	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12567600	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12758140	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17350523	0.95[JPT][hapmap]
rs2020862	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2064078	0.95[JPT][hapmap]
rs2075987	0.95[JPT][hapmap]
rs2075990	0.95[JPT][hapmap]
rs2075991	0.95[JPT][hapmap]
rs2179105	0.95[JPT][hapmap]
rs2205724	0.96[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2205729	0.95[JPT][hapmap]
rs2236874	0.96[JPT][hapmap]
rs2421709	0.81[ASN][1000 genomes]
rs28369823	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28369838	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28369839	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28369841	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28369847	0.95[ASN][1000 genomes]
rs3738813	0.96[JPT][hapmap]
rs3754495	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3768570	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6425394	0.95[JPT][hapmap]
rs6657314	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6662773	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6692347	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7513579	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7518899	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7531971	0.96[JPT][hapmap]
rs7534749	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7539549	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7540349	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7550060	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7555557	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs926268	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171153400-171159000	Active TSS	Aorta	Aorta
2	chr1:171154000-171159600	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr1:171154200-171158800	Active TSS	Psoas Muscle	Psoas
4	chr1:171154200-171159000	Active TSS	Left Ventricle	heart
5	chr1:171154200-171160800	Active TSS	Right Atrium	heart
6	chr1:171155000-171158000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:171156000-171158400	Enhancers	Fetal Lung	lung
8	chr1:171156400-171158000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:171156400-171165800	Weak transcription	Gastric	stomach
10	chr1:171156600-171158600	Weak transcription	Lung	lung
11	chr1:171156600-171163800	Weak transcription	Small Intestine	intestine
12	chr1:171156600-171169800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:171156600-171177200	Weak transcription	Esophagus	oesophagus
14	chr1:171156600-171179600	Weak transcription	NHLF	lung
15	chr1:171156800-171158200	Weak transcription	Fetal Intestine Small	intestine
16	chr1:171156800-171179600	Weak transcription	Right Ventricle	heart
17	chr1:171157200-171158000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:171157200-171158400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:171157400-171158000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:171157400-171159000	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr1:171157600-171157800	Enhancers	Ovary	ovary
22	chr1:171157600-171157800	Enhancers	Osteobl	bone
23	chr1:171157600-171158000	Enhancers	Liver	Liver
24	chr1:171157600-171158000	Enhancers	Brain Hippocampus Middle	brain
25	chr1:171157600-171160000	Enhancers	Fetal Intestine Large	intestine

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