Variant report

Variant	rs680944
Chromosome Location	chr21:40909715-40909716
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	chr21:40901121..40903929-chr21:40907917..40910902,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11088484	0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs12626648	0.91[ASN][1000 genomes]
rs12626661	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2837075	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs28644269	0.83[ASN][1000 genomes]
rs4372991	0.88[ASN][1000 genomes]
rs4818051	0.91[ASN][1000 genomes]
rs516888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527987	0.88[ASN][1000 genomes]
rs574863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs587935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs619766	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs626856	0.88[YRI][hapmap]
rs656582	0.88[ASN][1000 genomes]
rs656618	0.92[ASN][1000 genomes]
rs670316	0.90[ASN][1000 genomes]
rs681447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7410119	0.82[ASN][1000 genomes]
rs8127424	0.94[ASN][1000 genomes]
rs8128108	0.94[ASN][1000 genomes]
rs8130455	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1062088	chr21:40838027-40919253	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2756754	chr21:40857523-40966156	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2758820	chr21:40857523-40966156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv34779	chr21:40884871-40977473	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv433457	chr21:40900348-40964553	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1057956	chr21:40907707-41393396	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv544444	chr21:40907707-41393396	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv3382342	chr21:40909663-40909970	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40901200-40910200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr21:40907000-40909800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr21:40908200-40910200	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr21:40908200-40910400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr21:40908400-40909800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr21:40909000-40910400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr21:40909200-40909800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr21:40909200-40910400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr21:40909200-40910600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr21:40909200-40910600	Enhancers	Stomach Mucosa	stomach
11	chr21:40909200-40912200	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr21:40909400-40909800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr21:40909400-40910000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr21:40909400-40910200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr21:40909600-40909800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr21:40909600-40909800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr21:40909600-40909800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr21:40909600-40910000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr21:40909600-40910000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr21:40909600-40910400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr21:40909600-40910400	Enhancers	Fetal Intestine Large	intestine
22	chr21:40909600-40910600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr21:40909600-40910800	Enhancers	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links