Variant report

Variant	rs10064543
Chromosome Location	chr5:75839369-75839370
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	POLR2A	chr5:75838483-75840557	PBDE	blood:	n/a	n/a
2	RUNX3	chr5:75838732-75839565	GM12878	blood:	n/a	n/a
3	CTCF	chr5:75839162-75839528	GM12878	blood:	n/a	chr5:75839342-75839360
4	CTCF	chr5:75839219-75839399	GM12891	blood:	n/a	chr5:75839342-75839360
5	CTCF	chr5:75839280-75839430	WERI-Rb-1	eye:	n/a	chr5:75839342-75839360
6	CTCF	chr5:75839280-75839430	GM12878	blood:	n/a	chr5:75839342-75839360
7	CTCF	chr5:75839320-75839470	GM06990	blood:	n/a	chr5:75839342-75839360
8	TEAD4	chr5:75838470-75839588	K562	blood:	n/a	n/a
9	CHD2	chr5:75839331-75839444	GM12878	blood:	n/a	n/a
10	UBTF	chr5:75838914-75839480	K562	blood:	n/a	n/a
11	GATA1	chr5:75838187-75839958	K562	blood:	n/a	chr5:75839479-75839486 chr5:75839472-75839493 chr5:75839477-75839489 chr5:75838499-75838509 chr5:75839475-75839491 chr5:75838896-75838913 chr5:75839479-75839486 chr5:75839475-75839491 chr5:75839479-75839486 chr5:75839479-75839488 chr5:75839478-75839488
12	CTCF	chr5:75839280-75839430	GM12869	blood:	n/a	chr5:75839342-75839360
13	CTCF	chr5:75839320-75839470	GM12868	blood:	n/a	chr5:75839342-75839360
14	MAX	chr5:75838696-75839553	NB4	blood:	n/a	n/a
15	MAX	chr5:75838845-75839538	K562	blood:	n/a	n/a
16	MAZ	chr5:75838607-75839518	K562	blood:	n/a	n/a
17	CHD2	chr5:75839191-75839391	K562	blood:	n/a	n/a
18	ATF1	chr5:75838766-75839534	K562	blood:	n/a	n/a
19	CTCF	chr5:75839260-75839410	Caco-2	colon:	n/a	chr5:75839342-75839360
20	RUNX3	chr5:75838669-75839605	GM12878	blood:	n/a	n/a
21	CTCF	chr5:75839280-75839385	GM12892	blood:	n/a	chr5:75839342-75839360
22	EP300	chr5:75838659-75839600	K562	blood:	n/a	n/a
23	MTA3	chr5:75838802-75839518	GM12878	blood:	n/a	n/a
24	BHLHE40	chr5:75839322-75839547	K562	blood:	n/a	n/a
25	CTCF	chr5:75839300-75839450	HepG2	liver:	n/a	chr5:75839342-75839360
26	GATA1	chr5:75838375-75839559	PBDE	blood:	n/a	chr5:75839479-75839486 chr5:75839472-75839493 chr5:75839477-75839489 chr5:75838499-75838509 chr5:75839475-75839491 chr5:75838896-75838913 chr5:75839479-75839486 chr5:75839475-75839491 chr5:75839479-75839486 chr5:75839479-75839488 chr5:75839478-75839488
27	CTCF	chr5:75839264-75839408	K562	blood:	n/a	chr5:75839342-75839360
28	CTCF	chr5:75839176-75839447	K562	blood:	n/a	chr5:75839342-75839360
29	MYC	chr5:75838759-75839542	K562	blood:	n/a	n/a
30	MAX	chr5:75839140-75839573	K562	blood:	n/a	n/a
31	CTCF	chr5:75839198-75839379	Spleen_OC	spleen:	n/a	chr5:75839342-75839360
32	BHLHE40	chr5:75839001-75839405	GM12878	blood:	n/a	n/a
33	CTCF	chr5:75839250-75839458	GM19239	blood:	n/a	chr5:75839342-75839360
34	CTCF	chr5:75839270-75839440	GM12878	blood:	n/a	chr5:75839342-75839360
35	CCNT2	chr5:75838441-75839406	K562	blood:	n/a	chr5:75838896-75838916
36	CTCF	chr5:75839260-75839410	GM12871	blood:	n/a	chr5:75839342-75839360
37	SMC3	chr5:75839257-75839523	GM12878	blood:	n/a	n/a
38	CTCF	chr5:75839283-75839417	GM19240	blood:	n/a	chr5:75839342-75839360
39	EP300	chr5:75839232-75839432	GM12878	blood:	n/a	n/a
40	ATF2	chr5:75838932-75839432	GM12878	blood:	n/a	n/a
41	WRNIP1	chr5:75839191-75839391	GM12878	blood:	n/a	n/a
42	CTCF	chr5:75839227-75839434	GM19238	blood:	n/a	chr5:75839342-75839360
43	UBTF	chr5:75838923-75839414	K562	blood:	n/a	n/a
44	CTCF	chr5:75839280-75839430	GM12875	blood:	n/a	chr5:75839342-75839360
45	RCOR1	chr5:75838076-75839656	K562	blood:	n/a	n/a
46	JUND	chr5:75838714-75839487	K562	blood:	n/a	n/a

Variant related genes	Relation type
IQGAP2	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10044688	0.84[JPT][hapmap]
rs10065424	0.85[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap]
rs10080190	0.83[JPT][hapmap]
rs10942784	0.89[JPT][hapmap]
rs12513951	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13355881	0.85[CHB][hapmap]
rs2202113	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4704330	0.89[JPT][hapmap]
rs4704332	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs4704333	0.85[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap]
rs6453231	0.89[JPT][hapmap]
rs6453232	0.84[JPT][hapmap]
rs6869692	0.88[JPT][hapmap]
rs6875519	0.82[TSI][hapmap]
rs6889411	0.84[JPT][hapmap]
rs7722711	0.84[JPT][hapmap]
rs7731027	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9293687	0.85[CHB][hapmap]
rs9293688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9687487	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022032	chr5:75785106-75914003	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv598679	chr5:75823965-75914729	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription 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	2 gene(s)	inside rSNPs	diseases
3	nsv1023953	chr5:75831037-75913784	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026257	chr5:75831037-75914003	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1016823	chr5:75831037-75915905	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv598680	chr5:75839165-75914729	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75826800-75840000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr5:75830000-75841600	Enhancers	Stomach Mucosa	stomach
3	chr5:75832200-75840000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:75833600-75839800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:75835600-75839800	Weak transcription	Spleen	Spleen
6	chr5:75835600-75871200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:75836600-75839600	Weak transcription	HepG2	liver
8	chr5:75837400-75840600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr5:75837400-75842800	Enhancers	Liver	Liver
10	chr5:75837800-75840600	Enhancers	Fetal Lung	lung
11	chr5:75837800-75841200	Enhancers	Placenta	Placenta
12	chr5:75838000-75840400	Enhancers	Fetal Thymus	thymus
13	chr5:75838000-75840600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:75838200-75840200	Enhancers	Small Intestine	intestine
15	chr5:75838200-75840600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr5:75838200-75841400	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr5:75838400-75839400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:75838400-75840200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr5:75838400-75840200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:75838400-75840600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr5:75838400-75840600	Enhancers	Fetal Kidney	kidney
22	chr5:75838600-75839400	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr5:75838600-75839400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr5:75838600-75839600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr5:75838600-75839600	Enhancers	Fetal Stomach	stomach
26	chr5:75838600-75840000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr5:75838600-75840200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr5:75838600-75840400	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr5:75838600-75840400	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr5:75838600-75840600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr5:75838800-75839400	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr5:75838800-75839400	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr5:75838800-75839400	Active TSS	Adipose Nuclei	Adipose
34	chr5:75838800-75839400	Enhancers	Thymus	Thymus
35	chr5:75838800-75839400	Flanking Active TSS	K562	blood
36	chr5:75838800-75839600	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr5:75838800-75839600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:75838800-75839600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:75838800-75839800	Flanking Active TSS	GM12878-XiMat	blood
40	chr5:75838800-75840200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr5:75838800-75840200	Enhancers	Gastric	stomach
42	chr5:75839000-75839400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:75839000-75839400	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr5:75839000-75839400	Enhancers	Fetal Muscle Leg	muscle
45	chr5:75839000-75839400	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr5:75839000-75839400	Active TSS	Rectal Smooth Muscle	rectum
47	chr5:75839000-75839600	Enhancers	H9 Cell Line	embryonic stem cell
48	chr5:75839000-75840000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr5:75839000-75840200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr5:75839000-75840400	Enhancers	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links