Variant report

Variant	rs17028924
Chromosome Location	chr2:98308128-98308129
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	GATA3	chr2:98307590-98308935	MCF-7	breast:	n/a	n/a
2	GATA3	chr2:98307709-98308215	MCF-7	breast:	n/a	n/a
3	GATA3	chr2:98307510-98308194	MCF-7	breast:	n/a	n/a
4	CTBP2	chr2:98307565-98308295	H1-hESC	embryonic stem cell:	n/a	n/a
5	TCF12	chr2:98307479-98308133	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98262433..98263983-chr2:98307567..98310262,2	MCF-7	breast:
2	chr2:98307215..98309904-chr2:98310640..98314213,3	K562	blood:

Variant related genes	Relation type
LINC01125	TF binding region
ENSG00000228486	Chromatin interaction
ENSG00000135940	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17028435	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17028568	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17028640	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17028771	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs17029878	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs55757705	0.92[AFR][1000 genomes]
rs55766309	0.85[AFR][1000 genomes]
rs56717024	0.82[AFR][1000 genomes]
rs57183691	0.93[AFR][1000 genomes]
rs57875000	0.84[AFR][1000 genomes]
rs58383658	0.84[AFR][1000 genomes]
rs58753916	0.86[AFR][1000 genomes]
rs73959772	1.00[AFR][1000 genomes]
rs9678135	1.00[YRI][hapmap];1.00[AFR][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:22 , 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	chr2:98305600-98313600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:98306000-98322400	Weak transcription	Fetal Stomach	stomach
5	chr2:98307000-98313400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:98307400-98308400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:98307600-98308200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr2:98307600-98308200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr2:98307600-98308200	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr2:98307600-98308200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr2:98307600-98308200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr2:98307600-98308200	Enhancers	HMEC	breast
13	chr2:98307600-98308400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr2:98307600-98308600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr2:98307800-98308200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr2:98307800-98308200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:98307800-98308400	Enhancers	Fetal Muscle Trunk	muscle
18	chr2:98307800-98310800	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr2:98308000-98308200	Enhancers	Brain Substantia Nigra	brain
20	chr2:98308000-98308400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr2:98308000-98308600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:98308000-98308600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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