Variant report

Variant	rs35894204
Chromosome Location	chr4:653881-653882
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	SUZ12	chr4:653037-653961	H1-hESC	embryonic stem cell:	n/a	n/a
2	RCOR1	chr4:653851-653893	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:653558-655042	K562	blood:	n/a	n/a
4	POLR2A	chr4:653707-653902	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:641525..644066-chr4:652058..654958,2	K562	blood:
2	chr11:116512208..116512892-chr4:653530..654530,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242686	TF binding region
PDE6B	TF binding region

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10012461	0.85[EUR][1000 genomes]
rs10015198	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10018393	0.85[EUR][1000 genomes]
rs10024575	0.85[EUR][1000 genomes]
rs13101691	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13103955	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13104878	0.87[EUR][1000 genomes]
rs13107526	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13110755	0.87[EUR][1000 genomes]
rs13111179	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13114299	0.87[EUR][1000 genomes]
rs13116523	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13117283	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13118033	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13127213	0.96[EUR][1000 genomes]
rs13133935	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13136626	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13139052	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13139089	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13143415	0.91[EUR][1000 genomes]
rs13147797	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13150119	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28648408	0.85[EUR][1000 genomes]
rs28654405	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28682363	0.85[EUR][1000 genomes]
rs28687729	1.00[EUR][1000 genomes]
rs28754934	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34053163	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34075612	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34094325	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34096984	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34165278	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34293668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34363025	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34366493	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34391278	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34402770	1.00[EUR][1000 genomes]
rs34421911	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34477049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34568772	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34585712	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34587191	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34698095	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34953355	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34992186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35006826	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35137658	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35158410	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35207129	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35219160	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35270524	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35455427	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35535457	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35564967	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35621318	0.87[EUR][1000 genomes]
rs35621580	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35649145	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35694609	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35732782	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35794339	1.00[AFR][1000 genomes]
rs35843044	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35853545	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35869797	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35896648	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35925646	0.87[EUR][1000 genomes]
rs35935310	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35972513	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36060793	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36117387	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61760239	0.87[EUR][1000 genomes]
rs71602477	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602479	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602480	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602481	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602482	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602484	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602486	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602489	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602490	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71602492	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71602500	0.87[EUR][1000 genomes]
rs7657809	0.85[EUR][1000 genomes]
rs7672426	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7674091	0.85[EUR][1000 genomes]
rs7674895	0.85[EUR][1000 genomes]
rs7685281	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
19	esv3361501	chr4:651652-655150	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	esv3363115	chr4:651852-655150	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	esv3409588	chr4:652502-655300	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

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	chr4:642400-654600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:642800-657000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:643000-657000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:645800-656800	Weak transcription	Gastric	stomach
7	chr4:648400-657000	Weak transcription	Right Ventricle	heart
8	chr4:649800-655600	Weak transcription	Thymus	Thymus
9	chr4:650000-654000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:650000-654200	Enhancers	HepG2	liver
11	chr4:650800-656000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr4:651200-654400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:651400-656400	Weak transcription	Pancreas	Pancrea
14	chr4:651600-657000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:651600-657200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr4:651800-656800	Weak transcription	Primary B cells from cord blood	blood
17	chr4:652000-656800	Weak transcription	Fetal Lung	lung
18	chr4:652200-654000	Genic enhancers	Spleen	Spleen
19	chr4:652400-655200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:652400-656800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:652600-654000	Strong transcription	Brain Anterior Caudate	brain
22	chr4:652600-656800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:652600-656800	Weak transcription	Fetal Thymus	thymus
24	chr4:652800-654000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:652800-654400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:652800-654400	Strong transcription	Brain Substantia Nigra	brain
27	chr4:652800-656000	Strong transcription	Brain Germinal Matrix	brain
28	chr4:653000-654600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:653000-655600	Weak transcription	Lung	lung
30	chr4:653000-656800	Weak transcription	Fetal Heart	heart
31	chr4:653000-657000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:653200-654000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr4:653200-654600	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr4:653200-654600	Strong transcription	Fetal Intestine Small	intestine
35	chr4:653200-655600	Strong transcription	Dnd41	blood
36	chr4:653200-655800	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:653200-656200	Strong transcription	Fetal Brain Female	brain
38	chr4:653200-656400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:653200-656800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:653200-657000	Weak transcription	Fetal Kidney	kidney
41	chr4:653200-657000	Weak transcription	Ovary	ovary
42	chr4:653400-654000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:653400-656200	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr4:653400-656400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:653400-656600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr4:653400-656800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:653600-654000	Strong transcription	Fetal Brain Male	brain
48	chr4:653600-656800	Weak transcription	Brain Angular Gyrus	brain
49	chr4:653600-656800	Strong transcription	Fetal Stomach	stomach
50	chr4:653600-657000	Weak transcription	Primary T cells from cord blood	blood

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