Variant report

Variant	rs11909470
Chromosome Location	chr21:37705616-37705617
allele	C/T
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	GATA3	chr21:37705544-37705970	T-47D	breast:	n/a	n/a
2	POLR2A	chr21:37705411-37706021	K562	blood:	n/a	n/a
3	SIN3AK20	chr21:37705362-37705987	MCF-7	breast:	n/a	n/a
4	NR2F2	chr21:37705497-37705988	MCF-7	breast:	n/a	n/a
5	GATA3	chr21:37705518-37705988	T-47D	breast:	n/a	n/a
6	GATA3	chr21:37705370-37706001	MCF-7	breast:	n/a	n/a
7	POLR2A	chr21:37705507-37705875	K562	blood:	n/a	n/a
8	GATA3	chr21:37705460-37706020	MCF-7	breast:	n/a	n/a
9	POLR2A	chr21:37705506-37705762	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:37690897..37695461-chr21:37701805..37709412,12	MCF-7	breast:

Variant related genes	Relation type
MORC3	TF binding region
ENSG00000159256	Chromatin interaction
ENSG00000273199	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10483033	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11909757	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11910005	1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11910447	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11911904	0.89[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16994069	1.00[EUR][1000 genomes]
rs28688747	1.00[EUR][1000 genomes]
rs57154050	1.00[EUR][1000 genomes]
rs59261999	1.00[EUR][1000 genomes]
rs59270005	1.00[EUR][1000 genomes]
rs61094968	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73381587	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73381588	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73381599	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73381601	1.00[EUR][1000 genomes]
rs73383707	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383713	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383714	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383715	1.00[EUR][1000 genomes]
rs73383722	1.00[EUR][1000 genomes]
rs73385706	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33578	chr21:37488312-37819627	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv913734	chr21:37617630-37718587	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:37694200-37709600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr21:37694400-37709200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr21:37694400-37713000	Weak transcription	Esophagus	oesophagus
4	chr21:37694400-37713600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr21:37694400-37718200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr21:37694600-37706200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr21:37694600-37709000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr21:37695000-37706400	Weak transcription	Thymus	Thymus
9	chr21:37695000-37713800	Weak transcription	Fetal Brain Male	brain
10	chr21:37695800-37708800	Weak transcription	HSMMtube	muscle
11	chr21:37696000-37708600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr21:37697400-37706200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr21:37697400-37710200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr21:37697600-37706800	Weak transcription	Placenta	Placenta
15	chr21:37697800-37706000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr21:37698000-37706800	Weak transcription	Hela-S3	cervix
17	chr21:37698200-37705800	Enhancers	Liver	Liver
18	chr21:37698200-37708800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr21:37698600-37706400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr21:37699000-37705800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr21:37699000-37709200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr21:37699200-37707400	Genic enhancers	Primary T cells fromperipheralblood	blood
23	chr21:37699400-37757600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr21:37701200-37706200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr21:37701200-37750600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr21:37701600-37751400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr21:37701800-37706400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr21:37701800-37727000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr21:37702000-37708800	Weak transcription	NHLF	lung
30	chr21:37702000-37709000	Weak transcription	NH-A	brain
31	chr21:37702000-37711600	Weak transcription	Brain Angular Gyrus	brain
32	chr21:37702400-37706400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr21:37702600-37706200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr21:37702600-37706200	Weak transcription	Lung	lung
35	chr21:37702600-37706400	Weak transcription	Spleen	Spleen
36	chr21:37702600-37710000	Weak transcription	Colonic Mucosa	Colon
37	chr21:37702600-37710200	Weak transcription	Gastric	stomach
38	chr21:37702600-37713200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr21:37702600-37722000	Weak transcription	Right Atrium	heart
40	chr21:37702800-37706000	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr21:37702800-37706400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr21:37702800-37706400	Weak transcription	Brain Germinal Matrix	brain
43	chr21:37702800-37709200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr21:37703000-37705800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr21:37703000-37708400	Weak transcription	Pancreas	Pancrea
46	chr21:37703200-37706800	Weak transcription	HepG2	liver
47	chr21:37703200-37709400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr21:37703400-37706200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr21:37703400-37706200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr21:37703400-37706200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links