Variant report

Variant	rs250236
Chromosome Location	chr5:50266005-50266006
allele	A/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	BACH1	chr5:50265602-50266106	H1-hESC	embryonic stem cell:	n/a	n/a
2	SUZ12	chr5:50262485-50266469	NT2-D1	testis:	n/a	n/a
3	GATA2	chr5:50263552-50266094	SH-SY5Y	brain:	n/a	chr5:50264176-50264197 chr5:50264179-50264195 chr5:50264183-50264192 chr5:50264183-50264192 chr5:50264164-50264171 chr5:50263968-50263975 chr5:50264179-50264195 chr5:50264859-50264868 chr5:50264182-50264192 chr5:50266034-50266043
4	CTBP2	chr5:50265045-50266075	H1-hESC	embryonic stem cell:	n/a	n/a
5	REST	chr5:50261713-50266474	H1-neurons	neurons:	n/a	chr5:50264435-50264449 chr5:50264118-50264138 chr5:50264118-50264138 chr5:50265442-50265452 chr5:50264121-50264134
6	POLR2A	chr5:50264923-50266294	H1-neurons	neurons:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EMB-3	chr5:50265885-50266021	XLOC_004815
2	lnc-PARP8-2	chr5:50265885-50266021	ENSG00000248918
3	lnc-PARP8-2	chr5:50265757-50272447	NONHSAT101376
4	lnc-EMB-3	chr5:50265757-50266021	NR_104653

Variant related genes	Relation type
ENSG00000250360	TF binding region
ENSG00000251573	TF binding region

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10054384	1.00[ASN][1000 genomes]
rs10472047	0.81[ASN][1000 genomes]
rs16887696	1.00[ASN][1000 genomes]
rs16888239	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs185137	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs250233	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs250237	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs250238	0.82[AFR][1000 genomes]
rs4626298	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5005508	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55833214	1.00[ASN][1000 genomes]
rs6864779	1.00[ASN][1000 genomes]
rs72758259	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72758263	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72758266	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73752801	0.89[ASN][1000 genomes]
rs7703469	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717928	1.00[ASN][1000 genomes]
rs7725532	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7730386	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv830286	chr5:50165805-50374600	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50258600-50266600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr5:50261400-50266400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:50261400-50266400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr5:50262600-50266200	Bivalent/Poised TSS	Fetal Stomach	stomach
5	chr5:50262800-50266200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
6	chr5:50263800-50266200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr5:50263800-50266400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
8	chr5:50264600-50266200	Bivalent/Poised TSS	Fetal Thymus	thymus
9	chr5:50264800-50266200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr5:50264800-50266400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr5:50264800-50266600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr5:50265000-50266200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:50265000-50266400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr5:50265200-50266200	Bivalent/Poised TSS	Thymus	Thymus
15	chr5:50265400-50266200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
16	chr5:50265400-50266200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:50265400-50266200	Bivalent Enhancer	Fetal Brain Female	brain
18	chr5:50265600-50266200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
19	chr5:50265800-50266400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:50265800-50266400	Enhancers	Pancreas	Pancrea
21	chr5:50265800-50266600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
22	chr5:50266000-50266200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:50266000-50266200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:50266000-50266200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:50266000-50266200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
26	chr5:50266000-50266200	Enhancers	Placenta	Placenta
27	chr5:50266000-50266400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
28	chr5:50266000-50266400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr5:50266000-50270000	Active TSS	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links