Variant report

Variant	rs3850946
Chromosome Location	chr11:64835415-64835416
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr11:64834847-64835584	GM12878	blood:	n/a	n/a
2	MTA3	chr11:64834579-64835650	GM12878	blood:	n/a	n/a
3	NFIC	chr11:64834876-64835440	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:64832671..64835759-chr11:64851097..64853512,3	MCF-7	breast:
2	chr11:64784559..64786063-chr11:64835391..64837243,2	MCF-7	breast:
3	chr11:64813127..64817234-chr11:64832954..64835448,4	MCF-7	breast:
4	chr11:64780520..64784503-chr11:64834796..64838390,5	MCF-7	breast:

Variant related genes	Relation type
CDCA5	TF binding region
ENSG00000213465	Chromatin interaction
ENSG00000168060	Chromatin interaction
ENSG00000162300	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000146670	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1196043	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1206196	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs12362669	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12363102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1300845	0.83[CEU][hapmap]
rs1706937	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2507814	0.82[CEU][hapmap]
rs35661464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759041	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs3850947	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4258384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544944	0.97[ASN][1000 genomes]
rs566221	0.83[CEU][hapmap];0.84[YRI][hapmap]
rs769440	0.85[AFR][1000 genomes];0.90[ASN][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	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897709	chr11:64772545-64870779	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv897710	chr11:64772545-64885445	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv897711	chr11:64772545-64900270	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64822400-64850800	Weak transcription	Esophagus	oesophagus
2	chr11:64830000-64836800	Weak transcription	Spleen	Spleen
3	chr11:64830200-64835800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr11:64830800-64835600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr11:64833400-64835800	Enhancers	H1 Cell Line	embryonic stem cell
6	chr11:64833600-64845600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr11:64834000-64836400	Weak transcription	Fetal Intestine Small	intestine
8	chr11:64834000-64838400	Enhancers	GM12878-XiMat	blood
9	chr11:64834200-64835800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:64834200-64837400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:64834200-64850600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr11:64834400-64836000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:64834400-64845000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:64834600-64836800	Weak transcription	K562	blood
15	chr11:64834600-64843000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:64834600-64846200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:64834800-64835800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:64834800-64843000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:64834800-64843200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:64834800-64843400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:64834800-64843400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:64834800-64844800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:64834800-64845000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:64834800-64847800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr11:64835000-64838000	Enhancers	HepG2	liver
26	chr11:64835000-64843000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:64835000-64843200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr11:64835000-64843400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr11:64835200-64835600	Enhancers	Fetal Thymus	thymus
30	chr11:64835200-64844000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr11:64835400-64836400	Weak transcription	Fetal Intestine Large	intestine
32	chr11:64835400-64843200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr11:64835400-64845000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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