Variant report

Variant	rs17880400
Chromosome Location	chr7:100495530-100495531
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	JUND	chr7:100495517-100495717	K562	blood:	n/a	n/a
2	CEBPB	chr7:100495406-100495977	K562	blood:	n/a	n/a
3	TBP	chr7:100494762-100495659	K562	blood:	n/a	n/a
4	NR2F2	chr7:100494819-100496082	K562	blood:	n/a	n/a
5	JUN	chr7:100493191-100496118	K562	blood:	n/a	chr7:100494328-100494341 chr7:100493521-100493530
6	CTCF	chr7:100495500-100495650	SK-N-SH_RA	brain:	n/a	n/a
7	TRIM28	chr7:100495426-100496034	K562	blood:	n/a	n/a
8	CTCF	chr7:100493591-100495920	SK-N-SH	brain:	n/a	chr7:100494903-100494919 chr7:100494902-100494920 chr7:100494902-100494915 chr7:100494142-100494151 chr7:100494905-100494918 chr7:100494905-100494918 chr7:100494904-100494925
9	STAT5A	chr7:100495324-100496047	K562	blood:	n/a	chr7:100495619-100495633 chr7:100495622-100495631 chr7:100495621-100495630 chr7:100495607-100495630
10	MYC	chr7:100493631-100495749	K562	blood:	n/a	chr7:100493756-100493765 chr7:100494831-100494840 chr7:100493755-100493766
11	GATA2	chr7:100495402-100495919	K562	blood:	n/a	chr7:100495580-100495588 chr7:100495870-100495887 chr7:100495618-100495628 chr7:100495865-100495876
12	CBX3	chr7:100494678-100495986	K562	blood:	n/a	n/a
13	CHD2	chr7:100495513-100495797	K562	blood:	n/a	n/a
14	MXI1	chr7:100495474-100495839	K562	blood:	n/a	n/a
15	GATA2	chr7:100495330-100496040	K562	blood:	n/a	chr7:100495580-100495588 chr7:100495870-100495887 chr7:100495618-100495628 chr7:100495865-100495876
16	TEAD4	chr7:100494945-100496009	K562	blood:	n/a	n/a
17	REST	chr7:100495444-100495919	K562	blood:	n/a	n/a
18	MYC	chr7:100494792-100495715	K562	blood:	n/a	chr7:100494831-100494840
19	POLR2A	chr7:100495347-100496011	K562	blood:	n/a	n/a
20	MAFF	chr7:100495494-100495876	K562	blood:	n/a	n/a
21	GATA1	chr7:100495415-100495801	K562	blood:	n/a	chr7:100495580-100495588 chr7:100495618-100495628
22	EP300	chr7:100495373-100495881	K562	blood:	n/a	chr7:100495777-100495791
23	ZNF274	chr7:100495349-100495822	K562	blood:	n/a	n/a
24	GATA1	chr7:100495424-100496046	PBDE	blood:	n/a	chr7:100495580-100495588 chr7:100495870-100495887 chr7:100495618-100495628 chr7:100495865-100495876
25	MAX	chr7:100493568-100496026	K562	blood:	n/a	chr7:100493756-100493765 chr7:100494831-100494840 chr7:100493755-100493766
26	TEAD4	chr7:100494754-100495992	K562	blood:	n/a	n/a
27	IRF1	chr7:100495521-100495778	K562	blood:	n/a	n/a
28	SMC3	chr7:100494701-100495626	SK-N-SH	brain:	n/a	chr7:100494908-100494918 chr7:100494904-100494918
29	POLR2A	chr7:100494792-100495848	K562	blood:	n/a	n/a
30	PML	chr7:100495307-100495954	K562	blood:	n/a	n/a
31	MYC	chr7:100493573-100495803	K562	blood:	n/a	chr7:100493756-100493765 chr7:100494831-100494840 chr7:100493755-100493766
32	ZMIZ1	chr7:100495458-100495757	K562	blood:	n/a	n/a
33	EP300	chr7:100495407-100496014	K562	blood:	n/a	chr7:100495777-100495791
34	RCOR1	chr7:100495298-100495783	K562	blood:	n/a	n/a
35	TBL1XR1	chr7:100494878-100495777	K562	blood:	n/a	n/a
36	RFX5	chr7:100495398-100495828	K562	blood:	n/a	n/a
37	CCNT2	chr7:100495430-100495731	K562	blood:	n/a	n/a
38	BHLHE40	chr7:100495470-100495753	K562	blood:	n/a	n/a
39	CEBPD	chr7:100495315-100496057	K562	blood:	n/a	n/a
40	STAT5A	chr7:100495317-100496131	K562	blood:	n/a	chr7:100495619-100495633 chr7:100495622-100495631 chr7:100495621-100495630 chr7:100495607-100495630
41	RCOR1	chr7:100494998-100495779	K562	blood:	n/a	n/a
42	NR2F2	chr7:100495345-100495997	K562	blood:	n/a	n/a
43	TBL1XR1	chr7:100495435-100495851	K562	blood:	n/a	n/a
44	POLR2A	chr7:100493215-100495902	K562	blood:	n/a	n/a
45	POLR2A	chr7:100495384-100495935	K562	blood:	n/a	n/a
46	CEBPD	chr7:100495327-100495922	K562	blood:	n/a	n/a
47	TAL1	chr7:100494946-100496057	K562	blood:	n/a	chr7:100494981-100494996 chr7:100495570-100495588 chr7:100495869-100495887
48	CTCF	chr7:100495440-100495590	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:100494043..100496246-chr7:100550371..100552219,2	K562	blood:
2	chr7:100491420..100497264-chr7:100607951..100612175,9	K562	blood:
3	chr7:100491799..100497264-chr7:100607837..100612175,9	K562	blood:
4	chr7:100494780..100495608-chr7:100609169..100610066,2	MCF-7	breast:
5	chr7:100495042..100497121-chr7:100497583..100500198,2	MCF-7	breast:
6	chr7:100494449..100495718-chr7:100608430..100610036,6	MCF-7	breast:
7	chr7:100493490..100497118-chr7:100701265..100703603,3	K562	blood:
8	chr7:100026330..100028591-chr7:100493941..100496922,3	K562	blood:
9	chr7:100026330..100028332-chr7:100493941..100495752,2	K562	blood:
10	chr7:100494655..100497277-chr7:100728768..100731587,2	K562	blood:
11	chr7:100494864..100496737-chr7:100607538..100610305,2	MCF-7	breast:
12	chr7:100492733..100496183-chr7:100699112..100703676,5	MCF-7	breast:

Variant related genes	Relation type
ACHE	TF binding region
ENSG00000169871	Chromatin interaction
ENSG00000225946	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000169894	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000222636	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17162500	1.00[MEX][hapmap]
rs17162522	0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap]
rs17883552	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56970616	0.87[AMR][1000 genomes]
rs57066808	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57981438	0.87[AMR][1000 genomes]
rs58170575	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58629441	0.87[AMR][1000 genomes]
rs61700243	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription 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 miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv464647	chr7:100374087-100497131	Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv607965	chr7:100374087-100497131	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv1032673	chr7:100382250-100606794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
8	nsv888799	chr7:100406144-100497131	Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
9	nsv888801	chr7:100416250-100497131	Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
10	nsv464648	chr7:100422156-100518458	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
11	nsv607966	chr7:100422156-100518458	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
12	nsv831073	chr7:100425659-100544888	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
13	nsv888802	chr7:100484917-100495530	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
14	nsv888803	chr7:100486656-100497131	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
15	nsv888805	chr7:100486754-100498057	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
16	nsv888806	chr7:100488407-100495530	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
17	nsv888807	chr7:100490077-100498057	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv888808	chr7:100490981-100498057	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv888809	chr7:100491451-100495530	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	nsv888810	chr7:100492127-100495530	Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	nsv888811	chr7:100492127-100497131	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
22	nsv888812	chr7:100492127-100498057	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	nsv888813	chr7:100492322-100495530	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
24	nsv888814	chr7:100492357-100495530	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
25	nsv888815	chr7:100492357-100497131	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100494000-100495600	Bivalent Enhancer	Fetal Brain Male	brain
2	chr7:100494200-100495800	Bivalent Enhancer	Stomach Mucosa	stomach
3	chr7:100494600-100496400	Enhancers	Fetal Intestine Small	intestine
4	chr7:100494600-100498600	Weak transcription	Gastric	stomach
5	chr7:100494800-100495600	Bivalent Enhancer	Fetal Thymus	thymus
6	chr7:100494800-100495600	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr7:100495000-100495600	Enhancers	Pancreas	Pancrea
8	chr7:100495000-100496000	Flanking Active TSS	K562	blood
9	chr7:100495000-100498600	Weak transcription	Right Atrium	heart
10	chr7:100495200-100495600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr7:100495200-100495600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr7:100495200-100495600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:100495200-100495600	Enhancers	Brain Substantia Nigra	brain
14	chr7:100495200-100495600	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
15	chr7:100495200-100495800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
16	chr7:100495200-100495800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr7:100495200-100496000	Enhancers	Duodenum Mucosa	Duodenum
18	chr7:100495200-100496000	Enhancers	Placenta Amnion	Placenta Amnion
19	chr7:100495200-100496000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
20	chr7:100495200-100498400	Weak transcription	Liver	Liver
21	chr7:100495400-100495600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr7:100495400-100496200	Enhancers	Fetal Intestine Large	intestine
23	chr7:100495400-100499800	Weak transcription	Colonic Mucosa	Colon

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