Variant report

Variant	rs11940989
Chromosome Location	chr4:10262655-10262656
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	SMC3	chr4:10262543-10262688	Hela-S3	cervix:	n/a	chr4:10262577-10262591
2	CTCF	chr4:10262560-10262710	GM12864	blood:	n/a	chr4:10262578-10262587 chr4:10262575-10262593 chr4:10262577-10262598
3	CTCF	chr4:10262540-10262690	NB4	blood:	n/a	chr4:10262578-10262587 chr4:10262575-10262593 chr4:10262577-10262598
4	CTCF	chr4:10262600-10262750	HMEC	breast:	n/a	n/a
5	CTCF	chr4:10262532-10262673	NHEK	skin:	n/a	chr4:10262578-10262587 chr4:10262575-10262593 chr4:10262577-10262598
6	CTCF	chr4:10262453-10262662	HepG2	liver:	n/a	chr4:10262578-10262587 chr4:10262575-10262593 chr4:10262577-10262598
7	CTCF	chr4:10262600-10262750	GM12873	blood:	n/a	n/a
8	CTCF	chr4:10262540-10262690	GM12873	blood:	n/a	chr4:10262578-10262587 chr4:10262575-10262593 chr4:10262577-10262598
9	CTCF	chr4:10262560-10262710	GM12872	blood:	n/a	chr4:10262578-10262587 chr4:10262575-10262593 chr4:10262577-10262598
10	CTCF	chr4:10262356-10262760	K562	blood:	n/a	chr4:10262578-10262587 chr4:10262575-10262593 chr4:10262577-10262598
11	CTCF	chr4:10262640-10262790	GM12872	blood:	n/a	n/a
12	CTCF	chr4:10262396-10262667	H1-hESC	embryonic stem cell:	n/a	chr4:10262578-10262587 chr4:10262575-10262593 chr4:10262577-10262598
13	CTCF	chr4:10262580-10262730	HPAF	blood vessel:	n/a	n/a
14	CTCF	chr4:10262536-10262669	GM12892	blood:	n/a	chr4:10262578-10262587 chr4:10262575-10262593 chr4:10262577-10262598
15	RAD21	chr4:10262396-10262802	H1-hESC	embryonic stem cell:	n/a	chr4:10262576-10262595 chr4:10262769-10262776
16	RCOR1	chr4:10262514-10262714	K562	blood:	n/a	n/a
17	CTCF	chr4:10262640-10262790	GM12869	blood:	n/a	n/a
18	CTCF	chr4:10262520-10262670	AG10803	skin:	n/a	chr4:10262578-10262587 chr4:10262575-10262593 chr4:10262577-10262598
19	RAD21	chr4:10262488-10262674	HepG2	liver:	n/a	chr4:10262576-10262595
20	CTCF	chr4:10262475-10262725	K562	blood:	n/a	chr4:10262578-10262587 chr4:10262575-10262593 chr4:10262577-10262598
21	YY1	chr4:10262433-10262676	K562	blood:	n/a	n/a
22	CTCF	chr4:10262415-10262691	K562	blood:	n/a	chr4:10262578-10262587 chr4:10262575-10262593 chr4:10262577-10262598
23	CTCF	chr4:10262540-10262690	GM12864	blood:	n/a	chr4:10262578-10262587 chr4:10262575-10262593 chr4:10262577-10262598
24	CTCF	chr4:10262520-10262670	HCT-116	colon:	n/a	chr4:10262578-10262587 chr4:10262575-10262593 chr4:10262577-10262598
25	CTCF	chr4:10262430-10262736	K562	blood:	n/a	chr4:10262578-10262587 chr4:10262575-10262593 chr4:10262577-10262598
26	CTCF	chr4:10262540-10262690	GM12871	blood:	n/a	chr4:10262578-10262587 chr4:10262575-10262593 chr4:10262577-10262598

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:10181799..10184639-chr4:10262185..10264664,2	K562	blood:
2	chr4:10254361..10256671-chr4:10262474..10264248,2	K562	blood:

Variant related genes	Relation type
ENSG00000250040	TF binding region
ENSG00000250573	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10017178	1.00[AMR][1000 genomes]
rs10018961	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10020785	1.00[AMR][1000 genomes]
rs10024904	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10025247	1.00[AMR][1000 genomes]
rs10027966	1.00[EUR][1000 genomes]
rs10033320	1.00[AMR][1000 genomes]
rs10033429	1.00[AMR][1000 genomes]
rs10489074	0.85[YRI][hapmap]
rs11931780	1.00[EUR][1000 genomes]
rs11932167	1.00[EUR][1000 genomes]
rs11939276	1.00[EUR][1000 genomes]
rs11942813	1.00[EUR][1000 genomes]
rs2215688	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28402181	1.00[EUR][1000 genomes]
rs28451062	1.00[EUR][1000 genomes]
rs28523886	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28529184	1.00[AMR][1000 genomes]
rs28544414	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28579481	1.00[EUR][1000 genomes]
rs28636428	1.00[EUR][1000 genomes]
rs28657072	1.00[EUR][1000 genomes]
rs28666833	1.00[EUR][1000 genomes]
rs28686816	1.00[EUR][1000 genomes]
rs28713317	1.00[EUR][1000 genomes]
rs6449378	1.00[EUR][1000 genomes]
rs6824188	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6834540	1.00[EUR][1000 genomes]
rs6842500	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6844190	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6844617	0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6848728	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6849993	1.00[EUR][1000 genomes]
rs6857912	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6857978	0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7672432	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7675693	1.00[EUR][1000 genomes]
rs7676455	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7690268	1.00[EUR][1000 genomes]
rs9884403	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878681	chr4:9802853-10397327	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
2	nsv997941	chr4:9805223-10493388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
3	nsv1008649	chr4:9805223-10589802	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv1000587	chr4:9805223-10610752	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
5	nsv537022	chr4:9805223-10610752	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers 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	56 gene(s)	inside rSNPs	diseases
6	nsv1003454	chr4:9805223-10710990	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
7	nsv537023	chr4:9805223-10710990	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
8	nsv1004801	chr4:9814720-10674528	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
9	nsv537024	chr4:9814720-10674528	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
10	nsv931483	chr4:9814721-10716463	Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
11	nsv1009972	chr4:9903566-10710990	Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
12	nsv537027	chr4:9903566-10710990	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
13	esv2752052	chr4:9911872-10313111	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
14	nsv1010620	chr4:9937123-10686682	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
15	nsv530280	chr4:9947818-10940041	Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
16	nsv532706	chr4:9948018-10451450	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
17	nsv878691	chr4:9966477-10418078	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
18	nsv1013487	chr4:9972011-10320963	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
19	nsv869057	chr4:10013411-10875454	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
20	nsv997936	chr4:10040713-11009045	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
21	nsv428438	chr4:10058226-10273779	Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
22	nsv537033	chr4:10069805-10297561	Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
23	nsv537035	chr4:10103058-10297561	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
24	esv2752053	chr4:10124819-10270300	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
25	nsv593695	chr4:10138470-10345548	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
26	nsv432577	chr4:10174139-10285348	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
27	nsv1006512	chr4:10209934-10263774	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
28	nsv1000177	chr4:10212245-10557776	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
29	nsv537037	chr4:10212245-10557776	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
30	nsv1013360	chr4:10223836-10264888	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
31	nsv1007206	chr4:10229982-10362490	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
32	nsv593708	chr4:10240178-10271645	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
33	nsv593709	chr4:10260477-10281141	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
34	nsv998266	chr4:10261175-10276467	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:10261200-10263000	Enhancers	K562	blood
2	chr4:10261800-10263000	Enhancers	HMEC	breast
3	chr4:10262000-10263400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:10262000-10263400	Weak transcription	Fetal Thymus	thymus
5	chr4:10262000-10273800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:10262400-10262800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:10262600-10262800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:10262600-10262800	Enhancers	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links