Variant report

Variant	rs13408774
Chromosome Location	chr2:180118204-180118205
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180116382..180118315-chr2:180123410..180126262,2	MCF-7	breast:
2	chr2:180114644..180119395-chr2:180127594..180130471,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187231	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10172589	0.85[ASN][1000 genomes]
rs10173853	1.00[AMR][1000 genomes]
rs10176828	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10178559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10186707	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10205588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10207754	1.00[AMR][1000 genomes]
rs10208882	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10209875	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10210749	0.81[ASN][1000 genomes]
rs10221811	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12328593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12329222	0.81[AFR][1000 genomes]
rs12611473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12612427	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12613089	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12616452	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12618724	1.00[ASN][1000 genomes]
rs12622434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13382573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13383806	1.00[CHB][hapmap]
rs13387502	1.00[ASN][1000 genomes]
rs13391187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13394908	1.00[AMR][1000 genomes]
rs13395559	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13412820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13417112	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13422693	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13424092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13429191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16866630	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16866647	1.00[CHB][hapmap]
rs28508327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35041512	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6734127	1.00[AMR][1000 genomes]
rs7578417	1.00[CHB][hapmap]
rs7581898	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7588135	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7601965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7608106	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs9288024	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv834472	chr2:180091670-180220448	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180091800-180127200	Weak transcription	Fetal Lung	lung
2	chr2:180098600-180118600	Weak transcription	Pancreas	Pancrea
3	chr2:180102800-180127800	Weak transcription	Psoas Muscle	Psoas
4	chr2:180105600-180120000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:180110200-180124200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:180111200-180120400	Enhancers	Primary B cells from peripheral blood	blood
7	chr2:180112200-180120000	Weak transcription	Fetal Kidney	kidney
8	chr2:180112400-180126200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:180112600-180118400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:180112600-180125000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:180112600-180126800	Weak transcription	Hela-S3	cervix
12	chr2:180115400-180127600	Weak transcription	NHLF	lung
13	chr2:180116200-180118400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:180116200-180118600	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr2:180116200-180124400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:180116400-180118600	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr2:180116800-180118600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:180116800-180118800	Enhancers	Adipose Nuclei	Adipose
19	chr2:180116800-180124400	Enhancers	HepG2	liver
20	chr2:180117400-180126200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:180117600-180119000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:180117600-180119200	Weak transcription	Brain Anterior Caudate	brain
23	chr2:180117800-180119200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:180117800-180119200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:180117800-180119200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:180117800-180124400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:180117800-180126400	Weak transcription	Small Intestine	intestine
28	chr2:180118000-180119000	Weak transcription	Brain Angular Gyrus	brain
29	chr2:180118000-180119200	Enhancers	GM12878-XiMat	blood
30	chr2:180118000-180119400	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr2:180118000-180120200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr2:180118000-180125200	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:180118200-180118800	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:180118200-180119400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:180118200-180122400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:180118200-180122800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:180118200-180124800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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