Variant report

Variant	rs3935840
Chromosome Location	chr2:10236372-10236373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10234144..10239226-chr2:10260228..10264848,7	K562	blood:
2	chr2:10186093..10191010-chr2:10234656..10237838,4	K562	blood:
3	chr2:10234216..10236108-chr2:10236183..10239201,3	K562	blood:
4	chr2:10236324..10238791-chr2:10261804..10263852,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272524	Chromatin interaction
ENSG00000171848	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10177872	1.00[ASN][1000 genomes]
rs10929632	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11886661	1.00[ASN][1000 genomes]
rs12992149	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13400128	1.00[ASN][1000 genomes]
rs4302193	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321336	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4485541	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4569449	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669527	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669528	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6432058	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432060	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72786623	1.00[ASN][1000 genomes]
rs72786624	1.00[ASN][1000 genomes]
rs7587317	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587529	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602408	0.81[EUR][1000 genomes];1.00[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	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv1007965	chr2:10154960-10276125	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1014790	chr2:10156968-10274855	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv999019	chr2:10157762-10273232	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv873633	chr2:10175442-10266563	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
7	nsv1010706	chr2:10189219-10266995	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10231400-10236600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr2:10232000-10236800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr2:10232000-10236800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:10232000-10240200	Weak transcription	Right Atrium	heart
5	chr2:10232000-10242600	Weak transcription	Pancreas	Pancrea
6	chr2:10234000-10237600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:10234000-10237600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:10234200-10237000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr2:10234400-10238000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:10234400-10238000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:10234600-10238000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:10234600-10238000	Enhancers	NHEK	skin
13	chr2:10234800-10238000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:10234800-10238000	Enhancers	HMEC	breast
15	chr2:10235000-10236400	Weak transcription	Fetal Kidney	kidney
16	chr2:10235000-10237400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:10235800-10236800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:10236200-10236800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr2:10236200-10237600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:10236200-10238000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:10236200-10238000	Enhancers	Cortex derived primary cultured neurospheres	brain

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