Variant report

Variant	rs12600980
Chromosome Location	chr17:46187141-46187142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:46185296-46189875	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46184602..46186632-chr17:46186895..46189927,3	MCF-7	breast:
2	chr17:46175023..46180196-chr17:46181333..46189268,23	MCF-7	breast:
3	chr17:46185336..46187355-chr6:44217982..44220067,2	MCF-7	breast:
4	chr17:46124892..46127654-chr17:46182877..46187326,5	K562	blood:
5	chr17:46123538..46128867-chr17:46183649..46187295,7	MCF-7	breast:
6	chr17:46132648..46135293-chr17:46184683..46187431,2	K562	blood:
7	chr17:46124455..46126784-chr17:46185415..46187285,2	MCF-7	breast:
8	chr17:46125014..46129511-chr17:46182877..46189561,8	K562	blood:
9	chr17:46174648..46181471-chr17:46183317..46187457,20	MCF-7	breast:
10	chr17:46179911..46181951-chr17:46186605..46188187,2	K562	blood:

No data

Variant related genes	Relation type
SNX11	TF binding region
ENSG00000263412	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000108468	Chromatin interaction
ENSG00000002919	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1010228	0.92[ASN][1000 genomes]
rs1010230	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10853094	0.87[ASN][1000 genomes]
rs10853097	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11079806	0.85[ASN][1000 genomes]
rs11079807	0.81[ASN][1000 genomes]
rs11079808	1.00[ASN][1000 genomes]
rs11079809	0.92[ASN][1000 genomes]
rs11649919	0.91[ASN][1000 genomes]
rs11651097	0.91[ASN][1000 genomes]
rs11655407	0.91[ASN][1000 genomes]
rs11869625	0.81[ASN][1000 genomes]
rs12450620	0.89[ASN][1000 genomes]
rs12601350	0.86[EUR][1000 genomes]
rs12602131	0.86[EUR][1000 genomes]
rs12602670	0.86[EUR][1000 genomes]
rs12602948	0.81[ASN][1000 genomes]
rs12936369	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12936731	0.89[ASN][1000 genomes]
rs12939514	0.91[ASN][1000 genomes]
rs12941295	1.00[ASN][1000 genomes]
rs12943543	1.00[ASN][1000 genomes]
rs12946143	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12949879	0.84[ASN][1000 genomes]
rs12950213	0.96[ASN][1000 genomes]
rs12950402	1.00[ASN][1000 genomes]
rs12952163	0.91[ASN][1000 genomes]
rs1452662	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1452663	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1452665	0.81[ASN][1000 genomes]
rs1468270	0.82[ASN][1000 genomes]
rs16951519	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16953927	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16953941	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1860866	0.92[ASN][1000 genomes]
rs2023885	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2051821	0.91[ASN][1000 genomes]
rs208005	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs208008	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208009	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208011	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs208012	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs208015	0.84[ASN][1000 genomes]
rs208019	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2109983	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2109984	1.00[ASN][1000 genomes]
rs2229369	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2240119	0.86[EUR][1000 genomes]
rs2240120	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2240121	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2285863	0.85[ASN][1000 genomes]
rs2325783	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2325784	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2325804	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2325885	0.81[ASN][1000 genomes]
rs34980108	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs35361214	0.91[ASN][1000 genomes]
rs35688835	1.00[ASN][1000 genomes]
rs36071506	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3744346	0.92[ASN][1000 genomes]
rs3744347	0.95[ASN][1000 genomes]
rs3785737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3815472	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4794441	1.00[ASN][1000 genomes]
rs4794442	0.83[ASN][1000 genomes]
rs4794447	0.84[ASN][1000 genomes]
rs4794448	1.00[ASN][1000 genomes]
rs4794449	1.00[ASN][1000 genomes]
rs4794450	0.94[ASN][1000 genomes]
rs4794451	1.00[ASN][1000 genomes]
rs4794453	1.00[ASN][1000 genomes]
rs4995899	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55696440	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55920502	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58203448	0.91[ASN][1000 genomes]
rs58554000	0.88[EUR][1000 genomes]
rs58595405	0.91[ASN][1000 genomes]
rs58624511	0.89[ASN][1000 genomes]
rs62064953	0.99[ASN][1000 genomes]
rs6504024	0.91[ASN][1000 genomes]
rs6504025	0.91[ASN][1000 genomes]
rs6504031	1.00[ASN][1000 genomes]
rs6504032	0.98[ASN][1000 genomes]
rs6847	0.91[ASN][1000 genomes]
rs71356520	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71356521	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71369829	0.89[ASN][1000 genomes]
rs7209585	0.99[ASN][1000 genomes]
rs7209730	0.92[ASN][1000 genomes]
rs7212202	0.89[ASN][1000 genomes]
rs7213339	0.90[ASN][1000 genomes]
rs7217496	0.91[ASN][1000 genomes]
rs7218700	0.88[ASN][1000 genomes]
rs7220520	0.95[ASN][1000 genomes]
rs7221441	0.95[ASN][1000 genomes]
rs7222136	0.92[ASN][1000 genomes]
rs7224014	0.91[ASN][1000 genomes]
rs7224461	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72823528	0.86[EUR][1000 genomes]
rs72823532	0.86[EUR][1000 genomes]
rs72823533	0.86[EUR][1000 genomes]
rs741058	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs757353	0.86[EUR][1000 genomes]
rs8065670	1.00[ASN][1000 genomes]
rs8065993	1.00[ASN][1000 genomes]
rs8066049	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8066391	0.98[ASN][1000 genomes]
rs8069889	0.88[ASN][1000 genomes]
rs8071199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8075500	0.98[ASN][1000 genomes]
rs8076380	1.00[ASN][1000 genomes]
rs8077860	1.00[ASN][1000 genomes]
rs8078125	0.91[ASN][1000 genomes]
rs8079616	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8080662	1.00[ASN][1000 genomes]
rs875065	0.91[ASN][1000 genomes]
rs875066	0.91[ASN][1000 genomes]
rs9747001	0.90[ASN][1000 genomes]
rs978263	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807087	0.92[ASN][1000 genomes]
rs9890691	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9899275	0.89[ASN][1000 genomes]
rs9899461	0.89[ASN][1000 genomes]
rs9903692	0.84[ASN][1000 genomes]
rs9909933	0.81[ASN][1000 genomes]
rs9910516	1.00[ASN][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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	nsv112217	chr17:46182711-46190093	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12600980	CBX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46184400-46187200	Active TSS	GM12878-XiMat	blood
2	chr17:46185600-46191000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr17:46185800-46188200	Weak transcription	Left Ventricle	heart
4	chr17:46185800-46188200	Weak transcription	Pancreas	Pancrea
5	chr17:46185800-46190000	Weak transcription	Lung	lung
6	chr17:46185800-46193000	Weak transcription	Gastric	stomach
7	chr17:46185800-46195800	Weak transcription	Ovary	ovary
8	chr17:46186000-46187400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr17:46186000-46188400	Enhancers	Brain Substantia Nigra	brain
10	chr17:46186000-46189200	Weak transcription	Colonic Mucosa	Colon
11	chr17:46186000-46195200	Weak transcription	Aorta	Aorta
12	chr17:46186000-46196200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr17:46186000-46198600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr17:46186200-46187200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr17:46186200-46187200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr17:46186200-46187200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:46186200-46187400	Enhancers	Adipose Nuclei	Adipose
18	chr17:46186200-46187400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr17:46186200-46187600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr17:46186200-46187600	Weak transcription	Brain Anterior Caudate	brain
21	chr17:46186200-46187600	Weak transcription	Right Ventricle	heart
22	chr17:46186200-46187800	Enhancers	Primary B cells from peripheral blood	blood
23	chr17:46186200-46188200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr17:46186200-46188400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr17:46186200-46188600	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr17:46186200-46189000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr17:46186200-46189400	Weak transcription	Placenta	Placenta
28	chr17:46186200-46189600	Weak transcription	Fetal Muscle Leg	muscle
29	chr17:46186200-46189600	Weak transcription	Thymus	Thymus
30	chr17:46186200-46189800	Weak transcription	Fetal Stomach	stomach
31	chr17:46186200-46190000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr17:46186200-46190400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr17:46186200-46190400	Weak transcription	Esophagus	oesophagus
34	chr17:46186200-46190400	Weak transcription	Fetal Kidney	kidney
35	chr17:46186200-46190600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr17:46186200-46190600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr17:46186200-46192000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr17:46186200-46192600	Weak transcription	Colon Smooth Muscle	Colon
39	chr17:46186200-46192600	Weak transcription	A549	lung
40	chr17:46186200-46193800	Weak transcription	Fetal Lung	lung
41	chr17:46186200-46195000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr17:46186200-46195200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr17:46186200-46196200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr17:46186200-46198600	Weak transcription	Fetal Brain Male	brain
45	chr17:46186200-46203600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr17:46186400-46187200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr17:46186400-46187200	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr17:46186400-46187400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr17:46186400-46187400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr17:46186400-46187400	Enhancers	Primary B cells from cord blood	blood

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