Variant report

Variant	rs10016866
Chromosome Location	chr4:79092549-79092550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:79091323..79093499-chr4:79096107..79097895,2	MCF-7	breast:
2	chr4:78980297..78981139-chr4:79092342..79093264,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10000964	1.00[ASN][1000 genomes]
rs10005124	1.00[ASN][1000 genomes]
rs1502887	1.00[ASN][1000 genomes]
rs28367528	1.00[ASN][1000 genomes]
rs28520643	1.00[ASN][1000 genomes]
rs28546473	1.00[ASN][1000 genomes]
rs28723619	1.00[ASN][1000 genomes]
rs4340818	1.00[ASN][1000 genomes]
rs4859517	1.00[ASN][1000 genomes]
rs4859895	1.00[CHB][hapmap]
rs6533375	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6842322	1.00[ASN][1000 genomes]
rs72858745	1.00[ASN][1000 genomes]
rs9284616	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9284617	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9307331	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv879502	chr4:79052851-79144309	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv829977	chr4:79082318-79110300	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv999844	chr4:79092549-79165869	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10016866	SNX7	trans	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79071400-79096600	Weak transcription	Pancreas	Pancrea
2	chr4:79078200-79094200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:79078400-79095600	Weak transcription	Psoas Muscle	Psoas
4	chr4:79083800-79093000	Weak transcription	Fetal Heart	heart
5	chr4:79084200-79093000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:79085000-79093000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:79087200-79092800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:79089200-79095600	Weak transcription	Fetal Intestine Small	intestine
9	chr4:79090000-79095600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:79090200-79093000	Weak transcription	HepG2	liver
11	chr4:79090200-79093200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:79090200-79094400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr4:79090200-79104200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:79091400-79093600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:79091800-79092800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr4:79092000-79092600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr4:79092000-79093000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:79092200-79093000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:79092200-79095400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr4:79092200-79097000	Weak transcription	Fetal Kidney	kidney
21	chr4:79092400-79092800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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