Variant report

Variant	rs1860866
Chromosome Location	chr17:46201031-46201032
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46123246..46128677-chr17:46197755..46203630,8	MCF-7	breast:
2	chr17:46177666..46179488-chr17:46200620..46202273,2	MCF-7	breast:
3	chr17:46183960..46186242-chr17:46200589..46203810,3	K562	blood:
4	chr17:46198773..46201065-chr17:46205294..46206959,2	K562	blood:
5	chr17:46102851..46105550-chr17:46199872..46202014,2	MCF-7	breast:
6	chr17:46197608..46199562-chr17:46200754..46203056,2	MCF-7	breast:
7	chr17:46177057..46179428-chr17:46199731..46201687,2	MCF-7	breast:
8	chr17:46183569..46185892-chr17:46198700..46202089,3	K562	blood:
9	chr17:46187740..46191239-chr17:46199544..46202144,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000002919	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000108468	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs1002330	0.80[ASN][1000 genomes]
rs1010228	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1010230	1.00[ASN][1000 genomes]
rs10445377	0.80[ASN][1000 genomes]
rs10853094	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10853097	0.91[ASN][1000 genomes]
rs10853098	0.80[ASN][1000 genomes]
rs11079806	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11079807	0.84[AFR][1000 genomes]
rs11079808	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11079809	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11649919	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11651097	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11655407	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11869625	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12450620	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12600980	0.92[ASN][1000 genomes]
rs12602948	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12936369	0.91[ASN][1000 genomes]
rs12936731	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12939334	0.80[ASN][1000 genomes]
rs12939514	0.88[ASN][1000 genomes]
rs12941295	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12941830	0.80[ASN][1000 genomes]
rs12943543	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12946143	0.83[ASN][1000 genomes]
rs12946208	0.80[ASN][1000 genomes]
rs12947089	0.80[ASN][1000 genomes]
rs12949879	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12950213	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12950402	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12952163	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1316657	0.80[ASN][1000 genomes]
rs1452662	0.89[ASN][1000 genomes]
rs1452663	0.89[ASN][1000 genomes]
rs1452665	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1468270	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16951519	0.83[ASN][1000 genomes]
rs16953927	0.89[ASN][1000 genomes]
rs16953941	0.89[ASN][1000 genomes]
rs17681336	0.80[ASN][1000 genomes]
rs1860862	0.84[ASN][1000 genomes]
rs1860863	0.84[ASN][1000 genomes]
rs2021752	0.80[ASN][1000 genomes]
rs2041572	0.84[ASN][1000 genomes]
rs2051821	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs208005	0.93[ASN][1000 genomes]
rs208008	0.95[ASN][1000 genomes]
rs208009	0.95[ASN][1000 genomes]
rs208011	0.91[ASN][1000 genomes]
rs208012	0.91[ASN][1000 genomes]
rs208015	0.88[ASN][1000 genomes]
rs208019	0.93[ASN][1000 genomes]
rs2109983	1.00[ASN][1000 genomes]
rs2109984	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2229369	0.82[ASN][1000 genomes]
rs2240120	0.81[ASN][1000 genomes]
rs2240121	0.83[ASN][1000 genomes]
rs2285863	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2325783	0.83[ASN][1000 genomes]
rs2325784	0.94[ASN][1000 genomes]
rs2325804	0.95[ASN][1000 genomes]
rs2325885	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34949267	0.80[ASN][1000 genomes]
rs34980108	0.89[ASN][1000 genomes]
rs35361214	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35688835	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36071506	0.89[ASN][1000 genomes]
rs3744346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3744347	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3785737	0.88[ASN][1000 genomes]
rs3792692	0.80[ASN][1000 genomes]
rs3815472	0.95[ASN][1000 genomes]
rs3897789	0.80[ASN][1000 genomes]
rs3944039	0.84[ASN][1000 genomes]
rs4794441	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4794448	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4794449	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4794450	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4794451	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4794453	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4995899	0.83[ASN][1000 genomes]
rs55696440	0.91[ASN][1000 genomes]
rs55920502	0.83[ASN][1000 genomes]
rs58203448	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58595405	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58624511	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62064953	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6504024	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6504025	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6504031	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6504032	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67345313	0.80[ASN][1000 genomes]
rs6847	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71356520	0.98[ASN][1000 genomes]
rs71356521	0.93[ASN][1000 genomes]
rs71369829	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7209585	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7209730	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7212202	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7213339	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7217496	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7218700	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7220520	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7220922	0.80[ASN][1000 genomes]
rs7221441	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7222136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223867	0.80[ASN][1000 genomes]
rs7224014	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7224461	1.00[ASN][1000 genomes]
rs7225550	0.80[ASN][1000 genomes]
rs7225865	0.82[ASN][1000 genomes]
rs741058	1.00[ASN][1000 genomes]
rs758999	0.84[ASN][1000 genomes]
rs8065670	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8065993	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8066049	0.89[ASN][1000 genomes]
rs8066391	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8069889	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8071199	0.94[ASN][1000 genomes]
rs8075500	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8076380	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8077860	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8078125	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8079616	0.95[ASN][1000 genomes]
rs8080662	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs875065	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs875066	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9747001	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs978263	0.92[ASN][1000 genomes]
rs9807087	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889470	0.80[ASN][1000 genomes]
rs9890691	0.92[ASN][1000 genomes]
rs9899275	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9899461	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9903692	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9909933	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9910516	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1860866	SNX11	cis	Whole Blood	GTEx
rs1860866	SNX11	cis	Skin Sun Exposed Lower leg	GTEx
rs1860866	PNPO	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46186200-46203600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:46188200-46201200	Strong transcription	Fetal Intestine Small	intestine
3	chr17:46188200-46207400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr17:46188400-46201400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr17:46189000-46202600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr17:46189400-46204200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr17:46189600-46201800	Strong transcription	Fetal Muscle Leg	muscle
8	chr17:46189800-46202000	Strong transcription	Fetal Stomach	stomach
9	chr17:46190000-46201400	Strong transcription	Lung	lung
10	chr17:46190000-46204800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr17:46190200-46201600	Strong transcription	Liver	Liver
12	chr17:46190400-46201600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:46190400-46205000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr17:46190800-46201400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:46191200-46201800	Strong transcription	Adipose Nuclei	Adipose
16	chr17:46191200-46220800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr17:46191600-46204600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr17:46191800-46201200	Strong transcription	Fetal Intestine Large	intestine
19	chr17:46191800-46201600	Strong transcription	Primary T cells from cord blood	blood
20	chr17:46191800-46204600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr17:46192000-46201200	Strong transcription	Placenta	Placenta
22	chr17:46192200-46201200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr17:46192200-46201600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:46192200-46202400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:46192400-46201200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr17:46192400-46201200	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr17:46192400-46201200	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr17:46192400-46201400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr17:46192400-46201400	Strong transcription	Fetal Thymus	thymus
30	chr17:46192400-46201600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr17:46192400-46201600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr17:46192400-46204800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr17:46192400-46205400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr17:46192800-46205600	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr17:46193000-46201200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr17:46194200-46201200	Strong transcription	Stomach Smooth Muscle	stomach
37	chr17:46194400-46204600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr17:46194600-46201200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr17:46194800-46201400	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr17:46194800-46205000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr17:46195000-46201600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr17:46195400-46201200	Strong transcription	GM12878-XiMat	blood
43	chr17:46195400-46201400	Strong transcription	Primary B cells from cord blood	blood
44	chr17:46195600-46201600	Strong transcription	HSMMtube	muscle
45	chr17:46196000-46201400	Strong transcription	NHEK	skin
46	chr17:46196800-46202200	Weak transcription	Stomach Mucosa	stomach
47	chr17:46196800-46204800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr17:46196800-46208800	Weak transcription	K562	blood
49	chr17:46197800-46221000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr17:46198200-46201600	Strong transcription	Rectal Smooth Muscle	rectum

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