Variant report

Variant	rs2404354
Chromosome Location	chr1:223840398-223840399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223833118..223836523-chr1:223838327..223841763,4	MCF-7	breast:
2	chr1:223840282..223843675-chr1:223851675..223856291,7	MCF-7	breast:
3	chr1:223834427..223836360-chr1:223837595..223841642,3	MCF-7	breast:
4	chr1:223837812..223840547-chr1:223845364..223849589,4	K562	blood:
5	chr1:223827148..223829506-chr1:223840054..223841666,2	MCF-7	breast:
6	chr1:223836208..223847031-chr1:223849408..223858826,22	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203697	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10799298	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1108089	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12094613	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118128	0.90[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs12130866	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs12132899	0.80[CEU][hapmap]
rs12137025	0.80[CEU][hapmap]
rs1573980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17483760	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs6668723	0.87[JPT][hapmap]
rs9803664	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv873209	chr1:223707647-223846564	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv873210	chr1:223707647-223856414	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv873211	chr1:223707647-223867631	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1000199	chr1:223803545-223854859	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv873212	chr1:223807262-223853792	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1012050	chr1:223824652-223843610	Weak transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv535309	chr1:223824652-223843610	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223830400-223841800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:223833600-223850800	Weak transcription	Colonic Mucosa	Colon
3	chr1:223834200-223841800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:223834400-223841600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:223836600-223840800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:223837800-223840800	Enhancers	Fetal Lung	lung
7	chr1:223838000-223840800	Enhancers	Psoas Muscle	Psoas
8	chr1:223838200-223841400	Enhancers	Fetal Muscle Leg	muscle
9	chr1:223838200-223842600	Weak transcription	Lung	lung
10	chr1:223838200-223850800	Weak transcription	Fetal Stomach	stomach
11	chr1:223839200-223840400	Enhancers	HMEC	breast
12	chr1:223839200-223840600	Bivalent Enhancer	Dnd41	blood
13	chr1:223839200-223841800	Enhancers	Fetal Brain Male	brain
14	chr1:223839200-223843600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:223839400-223840400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:223839400-223841400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:223839600-223840400	Enhancers	NHEK	skin
18	chr1:223839600-223841000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:223839600-223841600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:223839600-223841600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:223839600-223841800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:223839600-223843000	Weak transcription	Fetal Intestine Large	intestine
23	chr1:223839800-223841200	Weak transcription	A549	lung
24	chr1:223839800-223841400	Enhancers	Fetal Thymus	thymus
25	chr1:223840000-223840400	Enhancers	Brain Germinal Matrix	brain
26	chr1:223840000-223840600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr1:223840000-223840800	Weak transcription	Stomach Mucosa	stomach
28	chr1:223840000-223841600	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr1:223840000-223843600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:223840200-223840400	Enhancers	Brain Angular Gyrus	brain
31	chr1:223840200-223840400	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr1:223840200-223840400	Flanking Active TSS	Brain Cingulate Gyrus	brain
33	chr1:223840200-223840400	Enhancers	Brain Hippocampus Middle	brain
34	chr1:223840200-223840400	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr1:223840200-223840600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:223840200-223840600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:223840200-223840600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:223840200-223840600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:223840200-223840600	Enhancers	Esophagus	oesophagus
40	chr1:223840200-223840800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:223840200-223841000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:223840200-223841000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:223840200-223841000	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr1:223840200-223841000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:223840200-223841000	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:223840200-223841000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:223840200-223841000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr1:223840200-223841000	Genic enhancers	Gastric	stomach
49	chr1:223840200-223841200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:223840200-223841200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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