Variant report

Variant	rs56815690
Chromosome Location	chr5:36244271-36244272
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	GATA3	chr5:36244131-36244851	T-47D	breast:	n/a	chr5:36244565-36244575 chr5:36244564-36244580 chr5:36244568-36244575

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:36150463..36155255-chr5:36239958..36244873,10	K562	blood:
2	chr5:36150467..36154483-chr5:36238242..36244873,13	K562	blood:

Variant related genes	Relation type
NADK2	TF binding region
ENSG00000201223	Chromatin interaction
ENSG00000145604	Chromatin interaction
ENSG00000164187	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10452459	1.00[EUR][1000 genomes]
rs10461961	0.86[ASN][1000 genomes]
rs10461962	0.86[ASN][1000 genomes]
rs10461965	0.86[ASN][1000 genomes]
rs10512641	1.00[EUR][1000 genomes]
rs10512642	0.86[ASN][1000 genomes]
rs10941282	0.86[ASN][1000 genomes]
rs10941283	0.88[ASN][1000 genomes]
rs10941284	0.88[ASN][1000 genomes]
rs11949914	1.00[EUR][1000 genomes]
rs11952545	1.00[EUR][1000 genomes]
rs11953540	1.00[EUR][1000 genomes]
rs11959495	1.00[EUR][1000 genomes]
rs11960054	1.00[EUR][1000 genomes]
rs12054662	0.86[ASN][1000 genomes]
rs12054682	0.84[ASN][1000 genomes]
rs12054958	0.86[ASN][1000 genomes]
rs12055219	0.86[ASN][1000 genomes]
rs12109571	1.00[EUR][1000 genomes]
rs12654720	0.98[ASN][1000 genomes]
rs12656102	0.98[ASN][1000 genomes]
rs12657110	0.86[ASN][1000 genomes]
rs12658779	0.98[ASN][1000 genomes]
rs1364013	0.86[ASN][1000 genomes]
rs1364014	0.86[ASN][1000 genomes]
rs1364015	0.86[ASN][1000 genomes]
rs1500223	1.00[EUR][1000 genomes]
rs1500225	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16902710	1.00[EUR][1000 genomes]
rs16902726	1.00[EUR][1000 genomes]
rs16902747	1.00[EUR][1000 genomes]
rs16902765	1.00[EUR][1000 genomes]
rs16902789	1.00[EUR][1000 genomes]
rs16902793	0.86[ASN][1000 genomes]
rs16902797	0.86[ASN][1000 genomes]
rs16902812	0.86[ASN][1000 genomes]
rs16902813	0.86[ASN][1000 genomes]
rs16902814	1.00[EUR][1000 genomes]
rs16902827	0.86[ASN][1000 genomes]
rs16902829	1.00[EUR][1000 genomes]
rs16902836	0.86[ASN][1000 genomes]
rs16902845	0.86[ASN][1000 genomes]
rs16902858	1.00[EUR][1000 genomes]
rs16902871	0.89[ASN][1000 genomes]
rs16902872	0.94[AFR][1000 genomes]
rs16902910	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16902911	0.94[ASN][1000 genomes]
rs16902936	1.00[EUR][1000 genomes]
rs1874182	1.00[EUR][1000 genomes]
rs1965840	1.00[EUR][1000 genomes]
rs2172777	1.00[EUR][1000 genomes]
rs2362981	1.00[EUR][1000 genomes]
rs3849785	0.85[ASN][1000 genomes]
rs3849787	0.86[ASN][1000 genomes]
rs3853244	1.00[EUR][1000 genomes]
rs3853245	1.00[EUR][1000 genomes]
rs3895887	1.00[EUR][1000 genomes]
rs3900936	0.84[ASN][1000 genomes]
rs4022390	1.00[EUR][1000 genomes]
rs4869470	0.86[ASN][1000 genomes]
rs4869471	0.86[ASN][1000 genomes]
rs4869472	0.86[ASN][1000 genomes]
rs4869624	0.86[ASN][1000 genomes]
rs4869627	0.86[ASN][1000 genomes]
rs4869628	0.86[ASN][1000 genomes]
rs4869629	0.86[ASN][1000 genomes]
rs4869630	0.86[ASN][1000 genomes]
rs4869633	1.00[ASN][1000 genomes]
rs4869637	0.93[ASN][1000 genomes]
rs57472443	1.00[EUR][1000 genomes]
rs58131800	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59754678	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60083069	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61209349	0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61656343	0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6451255	1.00[EUR][1000 genomes]
rs6451267	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6860085	0.87[AFR][1000 genomes]
rs6860896	1.00[EUR][1000 genomes]
rs6866069	1.00[EUR][1000 genomes]
rs6867280	1.00[EUR][1000 genomes]
rs6869324	1.00[EUR][1000 genomes]
rs6872883	1.00[EUR][1000 genomes]
rs6874771	1.00[EUR][1000 genomes]
rs6875875	1.00[EUR][1000 genomes]
rs6878587	1.00[EUR][1000 genomes]
rs6881555	1.00[EUR][1000 genomes]
rs6886540	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6887103	1.00[EUR][1000 genomes]
rs6894587	1.00[EUR][1000 genomes]
rs6896114	1.00[EUR][1000 genomes]
rs6896401	1.00[EUR][1000 genomes]
rs6896576	1.00[EUR][1000 genomes]
rs6897845	1.00[EUR][1000 genomes]
rs6898451	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73081933	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73081942	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73081945	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73748793	1.00[EUR][1000 genomes]
rs73751620	1.00[EUR][1000 genomes]
rs73751622	1.00[EUR][1000 genomes]
rs766065	1.00[EUR][1000 genomes]
rs7702340	1.00[EUR][1000 genomes]
rs7705125	1.00[EUR][1000 genomes]
rs7709624	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7710047	1.00[EUR][1000 genomes]
rs7718407	1.00[EUR][1000 genomes]
rs7719226	1.00[EUR][1000 genomes]
rs7719889	1.00[EUR][1000 genomes]
rs7723314	1.00[EUR][1000 genomes]
rs7725596	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7730301	0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7730829	1.00[EUR][1000 genomes]
rs7733484	1.00[EUR][1000 genomes]
rs878608	1.00[ASN][1000 genomes]
rs921022	1.00[EUR][1000 genomes]
rs9637790	0.86[ASN][1000 genomes]
rs991033	0.86[ASN][1000 genomes]
rs991034	0.86[ASN][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	nsv830262	chr5:36074311-36293872	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	63 gene(s)	inside rSNPs	diseases
2	nsv1015638	chr5:36203646-36312576	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36243000-36245800	Weak transcription	Ovary	ovary
2	chr5:36243200-36245800	Weak transcription	Placenta	Placenta
3	chr5:36243200-36246600	Weak transcription	Fetal Stomach	stomach
4	chr5:36243200-36247000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:36243200-36248000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:36243200-36252600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr5:36243400-36246800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:36243400-36252800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:36243400-36253200	Weak transcription	Aorta	Aorta
10	chr5:36243600-36244600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr5:36243800-36245000	Enhancers	Liver	Liver
12	chr5:36244000-36244400	Weak transcription	Primary T cells from cord blood	blood
13	chr5:36244200-36244400	Enhancers	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links