Variant report

Variant	rs7858659
Chromosome Location	chr9:94822146-94822147
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:94821053..94823320-chr9:94823986..94826593,3	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10820935	0.85[ASN][1000 genomes]
rs10820936	1.00[CEU][hapmap];0.85[MEX][hapmap];0.84[AMR][1000 genomes]
rs10820937	0.81[CEU][hapmap]
rs10820938	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs10992212	0.88[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992215	0.85[ASN][1000 genomes]
rs10992216	0.84[ASN][1000 genomes]
rs10992220	0.83[ASN][1000 genomes]
rs10992221	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992222	0.88[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992230	0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs10992233	0.83[ASN][1000 genomes]
rs10992234	0.81[CEU][hapmap];0.91[MEX][hapmap]
rs11533009	0.88[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs12235309	0.83[ASN][1000 genomes]
rs12235310	0.88[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs12235495	0.87[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs12237221	0.84[ASN][1000 genomes]
rs12237598	0.88[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs12238682	0.83[ASN][1000 genomes]
rs12337180	0.94[ASN][1000 genomes]
rs12343974	0.89[ASN][1000 genomes]
rs16908135	0.88[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs16908137	0.87[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1970121	0.81[CEU][hapmap];0.91[MEX][hapmap]
rs2096388	0.81[ASN][1000 genomes]
rs3858090	0.88[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4518728	0.88[ASN][1000 genomes]
rs58909848	0.85[ASN][1000 genomes]
rs59183854	0.85[ASN][1000 genomes]
rs59856128	0.85[ASN][1000 genomes]
rs6479399	0.81[MKK][hapmap]
rs6479403	0.84[AMR][1000 genomes]
rs7022553	0.84[ASN][1000 genomes]
rs7024583	0.84[AMR][1000 genomes]
rs7029539	0.81[CEU][hapmap];0.91[MEX][hapmap]
rs7033030	0.81[ASN][1000 genomes]
rs7034509	0.86[AFR][1000 genomes]
rs7847966	0.92[ASN][1000 genomes]
rs7849220	0.88[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7851910	0.85[EUR][1000 genomes]
rs7852067	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7856177	0.81[CEU][hapmap];0.91[MEX][hapmap]
rs7860518	0.91[CEU][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.84[AMR][1000 genomes]
rs7862826	0.88[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs7872515	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv831653	chr9:94692454-94867542	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	esv3324084	chr9:94821393-94830399	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
7	esv3482528	chr9:94821472-94830365	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
8	esv3482529	chr9:94821472-94830365	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7858659	CDK20	cis	parietal	SCAN
rs7858659	FANCC	cis	cerebellum	SCAN
rs7858659	SPTLC1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94805000-94823200	Strong transcription	Duodenum Mucosa	Duodenum
2	chr9:94805600-94822600	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr9:94805600-94823400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:94805800-94822800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr9:94806000-94823200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr9:94806800-94822400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr9:94806800-94822800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr9:94807200-94822600	Strong transcription	Primary T cells from cord blood	blood
9	chr9:94807200-94823000	Strong transcription	Primary B cells from cord blood	blood
10	chr9:94807200-94823200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr9:94807400-94822800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:94807600-94824600	Weak transcription	Fetal Brain Male	brain
13	chr9:94809600-94823600	Weak transcription	Colonic Mucosa	Colon
14	chr9:94810800-94860200	Weak transcription	Right Ventricle	heart
15	chr9:94811200-94822600	Strong transcription	Primary hematopoietic stem cells	blood
16	chr9:94811800-94828400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr9:94812200-94822400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr9:94812200-94832200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:94812400-94828400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr9:94815400-94822200	Strong transcription	Fetal Muscle Leg	muscle
21	chr9:94815400-94822600	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr9:94815400-94822600	Strong transcription	Placenta	Placenta
23	chr9:94815400-94823000	Strong transcription	Dnd41	blood
24	chr9:94815600-94822200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr9:94815600-94822800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr9:94815800-94822600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:94816000-94823400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr9:94816600-94822200	Strong transcription	K562	blood
29	chr9:94816600-94822600	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr9:94816600-94822600	Strong transcription	Fetal Thymus	thymus
31	chr9:94817000-94822600	Strong transcription	Left Ventricle	heart
32	chr9:94817200-94824800	Weak transcription	Brain Substantia Nigra	brain
33	chr9:94817400-94826200	Weak transcription	NHLF	lung
34	chr9:94817600-94822200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:94817600-94822200	Weak transcription	Fetal Stomach	stomach
36	chr9:94817600-94823400	Weak transcription	Brain Anterior Caudate	brain
37	chr9:94817600-94827000	Weak transcription	Small Intestine	intestine
38	chr9:94817600-94828000	Weak transcription	Gastric	stomach
39	chr9:94817600-94828000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr9:94817600-94828200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr9:94817600-94828400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr9:94817600-94828600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr9:94817800-94822800	Weak transcription	Fetal Brain Female	brain
44	chr9:94817800-94823200	Weak transcription	Colon Smooth Muscle	Colon
45	chr9:94817800-94825400	Weak transcription	HUVEC	blood vessel
46	chr9:94817800-94826800	Weak transcription	HSMMtube	muscle
47	chr9:94817800-94827000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr9:94817800-94877000	Weak transcription	Fetal Heart	heart
49	chr9:94818000-94824600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr9:94818000-94826200	Weak transcription	Hela-S3	cervix

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