Variant report

Variant	rs28742266
Chromosome Location	chr4:651369-651370
allele	A/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	POLR2A	chr4:651163-652297	K562	blood:	n/a	n/a
2	TCF3	chr4:651203-651851	GM12878	blood:	n/a	n/a
3	RXRA	chr4:651060-652413	H1-hESC	embryonic stem cell:	n/a	chr4:652317-652333
4	POLR2A	chr4:651059-651923	H1-hESC	embryonic stem cell:	n/a	n/a
5	RXRA	chr4:651307-652360	HepG2	liver:	n/a	chr4:652317-652333
6	NR2F2	chr4:651325-652481	HepG2	liver:	n/a	n/a
7	RXRA	chr4:651081-652578	HepG2	liver:	n/a	chr4:652317-652333
8	CBX3	chr4:651182-651820	K562	blood:	n/a	n/a
9	NR2F2	chr4:651086-652523	MCF-7	breast:	n/a	n/a
10	NR2F2	chr4:651141-652387	K562	blood:	n/a	n/a
11	ZBTB7A	chr4:651250-651624	K562	blood:	n/a	n/a
12	NR2F2	chr4:651092-652404	K562	blood:	n/a	n/a
13	RXRA	chr4:651082-652423	H1-hESC	embryonic stem cell:	n/a	chr4:652317-652333
14	POLR2A	chr4:651168-651870	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr4:651190-652340	GM12878	blood:	n/a	n/a
16	NR2C2	chr4:651264-652307	HepG2	liver:	n/a	n/a
17	POLR2A	chr4:651350-651665	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:649938..652851-chr4:653641..657433,6	K562	blood:
2	chr4:644162..647846-chr4:649268..652076,4	MCF-7	breast:
3	chr4:642131..644821-chr4:649750..652284,2	MCF-7	breast:
4	chr4:613849..616261-chr4:650426..653017,2	K562	blood:

Variant related genes	Relation type
ENSG00000242686	TF binding region
ENSG00000272927	Chromatin interaction
ENSG00000133256	Chromatin interaction
ENSG00000242686	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10027549	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030136	1.00[ASN][1000 genomes]
rs1135375	1.00[ASN][1000 genomes]
rs28407346	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs28470912	1.00[ASN][1000 genomes]
rs28483373	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28488910	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28525003	1.00[ASN][1000 genomes]
rs28568555	1.00[ASN][1000 genomes]
rs28569875	1.00[ASN][1000 genomes]
rs28573204	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28583078	1.00[ASN][1000 genomes]
rs28630797	1.00[ASN][1000 genomes]
rs28742899	1.00[ASN][1000 genomes]
rs3864130	1.00[ASN][1000 genomes]
rs3864131	1.00[ASN][1000 genomes]
rs3891250	1.00[ASN][1000 genomes]
rs4463020	1.00[ASN][1000 genomes]
rs4518182	1.00[ASN][1000 genomes]
rs58227539	1.00[ASN][1000 genomes]
rs60316402	1.00[ASN][1000 genomes]
rs71602496	1.00[ASN][1000 genomes]
rs73056602	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73058406	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7436737	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9985747	0.83[EUR][1000 genomes]
rs9991613	1.00[ASN][1000 genomes]
rs9992641	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
9	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS 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	104 gene(s)	inside rSNPs	diseases
14	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv4194	chr4:635316-657212	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv878248	chr4:645300-685993	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	nsv878249	chr4:649639-691026	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	esv3407640	chr4:650177-652725	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	esv3428482	chr4:651252-655450	Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28742266	RP11-1191J2.2	cis	Thyroid	GTEx
rs28742266	RP11-1191J2.2	cis	lung	GTEx
rs28742266	RP11-1191J2.2	cis	Nerve Tibial	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:631400-657000	Weak transcription	Right Atrium	heart
2	chr4:641800-657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:642200-652800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:642400-654600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:642800-657000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:643000-657000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:645800-656800	Weak transcription	Gastric	stomach
8	chr4:648400-657000	Weak transcription	Right Ventricle	heart
9	chr4:648800-653400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:649000-652800	Weak transcription	Brain Germinal Matrix	brain
11	chr4:649200-652800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:649200-653000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:649800-653200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:649800-655600	Weak transcription	Thymus	Thymus
15	chr4:650000-653200	Weak transcription	Fetal Brain Female	brain
16	chr4:650000-654000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr4:650000-654200	Enhancers	HepG2	liver
18	chr4:650200-652800	Weak transcription	Brain Substantia Nigra	brain
19	chr4:650600-652600	Weak transcription	Brain Anterior Caudate	brain
20	chr4:650600-652800	Weak transcription	Brain Angular Gyrus	brain
21	chr4:650800-652800	Weak transcription	Primary T cells from cord blood	blood
22	chr4:650800-656000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr4:651000-651400	Enhancers	Pancreas	Pancrea
24	chr4:651000-652800	Weak transcription	Brain Hippocampus Middle	brain
25	chr4:651000-653200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr4:651000-653600	Weak transcription	Fetal Brain Male	brain
27	chr4:651200-651400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:651200-652200	Enhancers	Spleen	Spleen
29	chr4:651200-653200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr4:651200-654400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links