Variant report

Variant	rs17517058
Chromosome Location	chr6:140201178-140201179
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	TEAD4	chr6:140201049-140201501	MCF-7	breast:	n/a	n/a
2	TEAD4	chr6:140201086-140201478	MCF-7	breast:	n/a	n/a
3	ZNF217	chr6:140201151-140201524	MCF-7	breast:	n/a	n/a
4	ESR1	chr6:140201019-140201593	T-47D	breast:	n/a	chr6:140201331-140201348 chr6:140201332-140201349
5	FOXM1	chr6:140201049-140201522	MCF-7	breast:	n/a	n/a
6	ESR1	chr6:140200953-140201592	T-47D	breast:	n/a	chr6:140201331-140201348 chr6:140201332-140201349
7	NR2F2	chr6:140200926-140201687	MCF-7	breast:	n/a	n/a
8	EP300	chr6:140201028-140201630	MCF-7	breast:	n/a	chr6:140201247-140201261 chr6:140201078-140201087
9	ESR1	chr6:140200874-140201625	T-47D	breast:	n/a	chr6:140201331-140201348 chr6:140201332-140201349
10	RAD21	chr6:140200959-140201473	MCF-7	breast:	n/a	n/a
11	JUND	chr6:140201083-140201624	MCF-7	breast:	n/a	n/a
12	GATA3	chr6:140201129-140201554	MCF-7	breast:	n/a	n/a
13	FOXM1	chr6:140200898-140201767	MCF-7	breast:	n/a	n/a
14	ESR1	chr6:140201009-140201615	T-47D	breast:	n/a	chr6:140201331-140201348 chr6:140201332-140201349
15	TCF12	chr6:140200946-140201649	MCF-7	breast:	n/a	chr6:140201575-140201582
16	SIN3AK20	chr6:140200810-140201786	MCF-7	breast:	n/a	n/a
17	GATA3	chr6:140201093-140201478	MCF-7	breast:	n/a	n/a
18	GATA3	chr6:140200744-140201707	MCF-7	breast:	n/a	chr6:140200750-140200757 chr6:140201079-140201089 chr6:140200750-140200757 chr6:140200750-140200757 chr6:140200750-140200760
19	TCF7L2	chr6:140201148-140201432	MCF-7	breast:	n/a	n/a
20	EP300	chr6:140201050-140201612	MCF-7	breast:	n/a	chr6:140201247-140201261 chr6:140201078-140201087
21	JUND	chr6:140200958-140201603	T-47D	breast:	n/a	n/a
22	ESR1	chr6:140200980-140201613	T-47D	breast:	n/a	chr6:140201331-140201348 chr6:140201332-140201349
23	ESR1	chr6:140201127-140201446	T-47D	breast:	n/a	chr6:140201331-140201348 chr6:140201332-140201349
24	GATA3	chr6:140200996-140201670	MCF-7	breast:	n/a	chr6:140201079-140201089
25	NR2F2	chr6:140200994-140201565	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:140200893..140201775-chr6:140298811..140299586,3	MCF-7	breast:
2	chr6:139757726..139758506-chr6:140200893..140201759,2	MCF-7	breast:
3	chr6:139692335..139698075-chr6:140197375..140205470,17	MCF-7	breast:
4	chr6:140199686..140202479-chr6:140203984..140206544,2	K562	blood:
5	chr6:139757726..139758506-chr6:140200893..140201759,3	MCF-7	breast:
6	chr6:139692969..139697282-chr6:140197638..140202883,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225148	TF binding region
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2051115	1.00[ASW][hapmap]
rs72986790	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17517058	TIMP1	trans	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140190800-140203400	Weak transcription	Fetal Lung	lung
2	chr6:140191600-140203000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:140194000-140201400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:140194400-140203000	Weak transcription	NHLF	lung
5	chr6:140194800-140204200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:140199400-140202400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:140199400-140202600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:140200600-140201200	Enhancers	Placenta	Placenta
9	chr6:140200800-140201400	Enhancers	Liver	Liver
10	chr6:140201000-140201200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:140201000-140201200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:140201000-140201200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:140201000-140201400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:140201000-140201400	Enhancers	Osteobl	bone
15	chr6:140201000-140201600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:140201000-140206400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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