Variant report

Variant	rs17028435
Chromosome Location	chr2:98305112-98305113
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	BATF	chr2:98304837-98305195	GM12878	blood:	n/a	n/a
2	BHLHE40	chr2:98304931-98305144	GM12878	blood:	n/a	n/a
3	RUNX3	chr2:98304526-98305475	GM12878	blood:	n/a	n/a
4	SP1	chr2:98304723-98305218	GM12878	blood:	n/a	n/a
5	ATF2	chr2:98304852-98305214	GM12878	blood:	n/a	n/a
6	NFIC	chr2:98304784-98305311	GM12878	blood:	n/a	n/a
7	TBL1XR1	chr2:98305002-98305432	GM12878	blood:	n/a	n/a
8	RCOR1	chr2:98304943-98305141	GM12878	blood:	n/a	n/a
9	FOXM1	chr2:98304841-98305286	GM12878	blood:	n/a	n/a
10	MAZ	chr2:98304962-98305144	GM12878	blood:	n/a	chr2:98305021-98305030
11	IRF4	chr2:98304418-98305179	GM12878	blood:	n/a	n/a
12	JUND	chr2:98304876-98305194	HepG2	liver:	n/a	chr2:98305021-98305029 chr2:98305020-98305029 chr2:98305020-98305030 chr2:98304980-98304991 chr2:98305021-98305030 chr2:98305022-98305029 chr2:98305019-98305030
13	FOSL2	chr2:98304837-98305163	HepG2	liver:	n/a	chr2:98305021-98305029 chr2:98305020-98305029 chr2:98305020-98305030 chr2:98305021-98305030 chr2:98305022-98305029
14	PML	chr2:98304659-98305283	GM12878	blood:	n/a	chr2:98304691-98304699 chr2:98305022-98305031
15	STAT3	chr2:98304799-98305267	GM12878	blood:	n/a	chr2:98305020-98305029 chr2:98305163-98305183 chr2:98305163-98305183 chr2:98305021-98305030
16	FOSL2	chr2:98304803-98305162	MCF-7	breast:	n/a	chr2:98305021-98305029 chr2:98305020-98305029 chr2:98305020-98305030 chr2:98305021-98305030 chr2:98305022-98305029
17	FOS	chr2:98304864-98305164	MCF10A-Er-Src	breast:	n/a	chr2:98305021-98305029 chr2:98305020-98305029 chr2:98305020-98305030 chr2:98305021-98305030 chr2:98305022-98305029
18	ATF2	chr2:98304789-98305264	GM12878	blood:	n/a	n/a
19	EP300	chr2:98304906-98305168	GM12878	blood:	n/a	chr2:98305020-98305029 chr2:98305021-98305030
20	RUNX3	chr2:98304879-98305187	GM12878	blood:	n/a	n/a
21	ELK1	chr2:98305036-98305156	GM12878	blood:	n/a	n/a
22	NFIC	chr2:98304442-98305340	GM12878	blood:	n/a	n/a
23	CREB1	chr2:98304807-98305240	GM12878	blood:	n/a	n/a
24	BATF	chr2:98304488-98305195	GM12878	blood:	n/a	n/a
25	SMC3	chr2:98304943-98305141	GM12878	blood:	n/a	n/a
26	FOS	chr2:98304871-98305259	MCF10A-Er-Src	breast:	n/a	chr2:98305021-98305029 chr2:98305020-98305029 chr2:98305020-98305030 chr2:98305021-98305030 chr2:98305022-98305029
27	FOS	chr2:98304874-98305171	MCF10A-Er-Src	breast:	n/a	chr2:98305021-98305029 chr2:98305020-98305029 chr2:98305020-98305030 chr2:98305021-98305030 chr2:98305022-98305029
28	FOS	chr2:98304831-98305191	MCF10A-Er-Src	breast:	n/a	chr2:98305021-98305029 chr2:98305020-98305029 chr2:98305020-98305030 chr2:98305021-98305030 chr2:98305022-98305029

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98279098..98281561-chr2:98304916..98307735,3	MCF-7	breast:
2	chr2:98278665..98281371-chr2:98305087..98308005,4	MCF-7	breast:

Variant related genes	Relation type
LINC01125	TF binding region
ENSG00000201806	Chromatin interaction
ENSG00000115073	Chromatin interaction
ENSG00000228486	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10460480	1.00[AMR][1000 genomes]
rs17022096	1.00[AMR][1000 genomes]
rs17022495	1.00[AMR][1000 genomes]
rs17028568	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17028640	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17028771	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs17028924	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17029878	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17031009	1.00[AMR][1000 genomes]
rs2167008	1.00[AMR][1000 genomes]
rs55637939	1.00[AMR][1000 genomes]
rs55757705	0.92[AFR][1000 genomes]
rs55766309	0.85[AFR][1000 genomes]
rs56045386	1.00[AMR][1000 genomes]
rs56381875	1.00[AMR][1000 genomes]
rs56717024	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56894046	1.00[AMR][1000 genomes]
rs57002448	1.00[AMR][1000 genomes]
rs57183691	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57875000	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58059561	1.00[AMR][1000 genomes]
rs58383658	0.84[AFR][1000 genomes]
rs58753916	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59134572	1.00[AMR][1000 genomes]
rs59340312	1.00[AMR][1000 genomes]
rs60599690	1.00[AMR][1000 genomes]
rs60713338	1.00[AMR][1000 genomes]
rs61016336	1.00[AMR][1000 genomes]
rs72951140	1.00[AMR][1000 genomes]
rs73959761	1.00[AMR][1000 genomes]
rs73959772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9678135	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
2	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
3	esv1829350	chr2:98170405-98315611	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98281000-98323800	Weak transcription	Gastric	stomach
2	chr2:98292200-98317800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:98303400-98305400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:98304600-98305400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:98304800-98305200	Flanking Active TSS	GM12878-XiMat	blood
6	chr2:98304800-98305400	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr2:98304800-98305600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr2:98304800-98305600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr2:98305000-98305200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:98305000-98305200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:98305000-98305400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:98305000-98305600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr2:98305000-98305600	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr2:98305000-98307600	Weak transcription	HMEC	breast

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