Variant report

Variant	rs12092242
Chromosome Location	chr1:171161498-171161499
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171157094..171159925-chr1:171161242..171162761,2	K562	blood:
2	chr1:171151483..171154581-chr1:171157949..171161924,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000094963	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10798263	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10798271	0.96[EUR][1000 genomes]
rs10912529	0.81[ASN][1000 genomes]
rs10912537	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10912538	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10912552	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10912593	0.96[EUR][1000 genomes]
rs11810116	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12061191	0.93[EUR][1000 genomes]
rs12085225	0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12566823	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12567059	0.96[ASN][1000 genomes]
rs12567358	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12567600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730305	0.81[ASN][1000 genomes]
rs12758140	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2205724	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2223228	0.81[ASN][1000 genomes]
rs28369823	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28369838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28369839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28369841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28369847	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754495	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3768569	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6662773	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6692347	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7513579	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7518899	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7534749	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7535566	0.95[EUR][1000 genomes]
rs7535771	0.96[EUR][1000 genomes]
rs7538013	0.81[ASN][1000 genomes]
rs7539549	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540349	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7550060	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555557	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171156400-171165800	Weak transcription	Gastric	stomach
2	chr1:171156600-171163800	Weak transcription	Small Intestine	intestine
3	chr1:171156600-171169800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:171156600-171177200	Weak transcription	Esophagus	oesophagus
5	chr1:171156600-171179600	Weak transcription	NHLF	lung
6	chr1:171156800-171179600	Weak transcription	Right Ventricle	heart
7	chr1:171157800-171165600	Weak transcription	Ovary	ovary
8	chr1:171158200-171167000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:171158400-171165600	Weak transcription	Fetal Lung	lung
10	chr1:171159000-171162000	Enhancers	Adipose Nuclei	Adipose
11	chr1:171159000-171165800	Weak transcription	Lung	lung
12	chr1:171160000-171164800	Weak transcription	Fetal Intestine Small	intestine
13	chr1:171160000-171165000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:171160200-171166800	Weak transcription	Fetal Brain Male	brain
15	chr1:171160400-171161800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:171160600-171163600	Weak transcription	Fetal Intestine Large	intestine
17	chr1:171160800-171161800	Enhancers	Liver	Liver
18	chr1:171161000-171162000	Weak transcription	Stomach Mucosa	stomach
19	chr1:171161000-171165800	Weak transcription	Aorta	Aorta
20	chr1:171161000-171171800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr1:171161200-171162000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:171161200-171162600	Enhancers	Right Atrium	heart
23	chr1:171161200-171163600	Weak transcription	Left Ventricle	heart
24	chr1:171161200-171165000	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links