Variant report

Variant	rs2109983
Chromosome Location	chr17:46207148-46207149
allele	C/T
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46102745..46105471-chr17:46206069..46210163,5	K562	blood:
2	chr17:46206531..46208867-chr17:46695496..46698467,2	K562	blood:
3	chr17:46109579..46112483-chr17:46205797..46208470,2	K562	blood:
4	chr17:46202062..46204690-chr17:46205157..46208075,2	K562	blood:
5	chr17:46101075..46105793-chr17:46203518..46208640,6	MCF-7	breast:
6	chr17:46202062..46204213-chr17:46205157..46207474,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNX11-7	chr17:46206813-46208268	NONHSAT054386

No data

Variant related genes	Relation type
ENSG00000005243	Chromatin interaction

Extended variants
information (count: 161 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs1002330	0.80[ASN][1000 genomes]
rs1010228	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1010230	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10445377	0.80[ASN][1000 genomes]
rs10853097	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10853098	0.80[ASN][1000 genomes]
rs11079806	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11079808	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11079809	1.00[ASN][1000 genomes]
rs11649919	0.83[ASN][1000 genomes]
rs11651097	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11655407	0.83[ASN][1000 genomes]
rs12450620	0.81[ASN][1000 genomes]
rs12600980	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12936369	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12936731	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12939334	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12939514	0.88[ASN][1000 genomes]
rs12941295	0.92[ASN][1000 genomes]
rs12941830	0.80[ASN][1000 genomes]
rs12943543	0.92[ASN][1000 genomes]
rs12946143	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12946208	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12946679	0.81[YRI][hapmap]
rs12947089	0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs12948214	1.00[YRI][hapmap]
rs12950213	0.88[ASN][1000 genomes]
rs12950402	0.92[ASN][1000 genomes]
rs12952163	0.83[ASN][1000 genomes]
rs1316657	0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs1452662	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1452663	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1452665	0.92[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs1452666	0.81[JPT][hapmap]
rs1452667	0.80[JPT][hapmap]
rs1468270	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs16951519	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16952687	1.00[YRI][hapmap]
rs16953927	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16953941	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16954268	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs16954324	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs17620033	0.80[JPT][hapmap]
rs17681336	0.80[ASN][1000 genomes]
rs1860862	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1860863	0.84[ASN][1000 genomes]
rs1860866	1.00[ASN][1000 genomes]
rs1979897	0.89[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2021752	0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs2023885	0.89[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2041572	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2051821	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2060876	0.81[JPT][hapmap]
rs208005	0.80[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs208008	0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs208009	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs208011	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs208012	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs208015	0.92[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs208019	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2109982	0.81[JPT][hapmap]
rs2109984	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2123341	0.80[JPT][hapmap]
rs2229369	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2240120	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2240121	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2240122	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2278868	0.80[JPT][hapmap]
rs2305433	0.80[JPT][hapmap]
rs2325783	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2325784	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2325804	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2325885	0.89[ASN][1000 genomes]
rs34949267	0.80[ASN][1000 genomes]
rs34980108	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35361214	0.83[ASN][1000 genomes]
rs35688835	0.92[ASN][1000 genomes]
rs36071506	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3744346	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3744347	0.88[ASN][1000 genomes]
rs3785737	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3792692	0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs3792694	0.80[JPT][hapmap]
rs3805370	0.85[CHB][hapmap]
rs3815472	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3897789	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3897986	0.80[JPT][hapmap]
rs3944039	0.84[ASN][1000 genomes]
rs4794441	0.92[ASN][1000 genomes]
rs4794447	0.81[JPT][hapmap]
rs4794448	0.92[ASN][1000 genomes]
rs4794449	0.92[ASN][1000 genomes]
rs4794450	0.87[ASN][1000 genomes]
rs4794451	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4794453	0.92[ASN][1000 genomes]
rs4995899	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55696440	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55920502	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58203448	0.83[ASN][1000 genomes]
rs58554000	0.81[EUR][1000 genomes]
rs58595405	0.83[ASN][1000 genomes]
rs58624511	0.81[ASN][1000 genomes]
rs62064953	0.91[ASN][1000 genomes]
rs6504024	0.83[ASN][1000 genomes]
rs6504025	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6504031	0.92[ASN][1000 genomes]
rs6504032	0.90[ASN][1000 genomes]
rs6504108	0.80[JPT][hapmap]
rs67345313	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6847	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs71356520	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71356521	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71369829	0.81[ASN][1000 genomes]
rs7209585	0.91[ASN][1000 genomes]
rs7209730	1.00[ASN][1000 genomes]
rs7212202	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7213339	0.87[ASN][1000 genomes]
rs7217496	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7218700	0.96[ASN][1000 genomes]
rs7220520	0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7220768	0.80[JPT][hapmap]
rs7220922	0.80[ASN][1000 genomes]
rs7221441	0.88[ASN][1000 genomes]
rs7222136	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7223867	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs7224014	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7224461	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7225550	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs7225865	0.82[ASN][1000 genomes]
rs741058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758999	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs8065670	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8065993	0.92[ASN][1000 genomes]
rs8066049	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8066391	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8069263	0.81[JPT][hapmap]
rs8069889	0.81[ASN][1000 genomes]
rs8071199	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8071879	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs8072282	0.80[JPT][hapmap]
rs8075500	0.90[ASN][1000 genomes]
rs8076380	0.92[ASN][1000 genomes]
rs8077860	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8078125	0.83[ASN][1000 genomes]
rs8079616	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8080662	0.92[ASN][1000 genomes]
rs875065	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs875066	0.83[ASN][1000 genomes]
rs9747001	0.82[ASN][1000 genomes]
rs978263	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9807087	1.00[ASN][1000 genomes]
rs9889470	0.80[ASN][1000 genomes]
rs9890691	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9899275	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9899461	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9903692	0.91[ASN][1000 genomes]
rs9909933	0.89[ASN][1000 genomes]
rs9910516	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2109983	CBX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46188200-46207400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:46191200-46220800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:46196800-46208800	Weak transcription	K562	blood
4	chr17:46197800-46221000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr17:46199400-46212400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:46199800-46209600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr17:46200400-46236600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr17:46200600-46209000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr17:46200600-46209600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr17:46200800-46207400	Weak transcription	Right Ventricle	heart
11	chr17:46200800-46208400	Weak transcription	Colon Smooth Muscle	Colon
12	chr17:46200800-46209000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr17:46200800-46212400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr17:46201000-46207600	Weak transcription	Dnd41	blood
15	chr17:46201200-46208000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr17:46201200-46209600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr17:46201400-46207600	Weak transcription	Fetal Kidney	kidney
18	chr17:46201400-46208400	Weak transcription	Brain Angular Gyrus	brain
19	chr17:46201400-46217600	Weak transcription	Fetal Thymus	thymus
20	chr17:46203000-46217000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr17:46203800-46209000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr17:46204000-46220000	Weak transcription	GM12878-XiMat	blood
23	chr17:46204200-46208000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr17:46204200-46210800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr17:46204200-46216600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr17:46204200-46225200	Weak transcription	Liver	Liver
27	chr17:46204400-46207800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:46204400-46221000	Weak transcription	Thymus	Thymus
29	chr17:46204600-46208800	Weak transcription	Adipose Nuclei	Adipose
30	chr17:46204600-46209600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr17:46204600-46209600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr17:46204600-46209600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr17:46204600-46216600	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr17:46204600-46217000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr17:46204800-46207200	Weak transcription	Primary T cells from cord blood	blood
36	chr17:46204800-46209600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr17:46205000-46207400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr17:46205000-46207400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr17:46205000-46214600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr17:46205000-46215400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr17:46205000-46216800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr17:46205000-46217400	Weak transcription	Primary B cells from cord blood	blood
43	chr17:46205200-46208000	Weak transcription	Fetal Intestine Small	intestine
44	chr17:46205200-46208400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr17:46205400-46207200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr17:46205400-46208000	Weak transcription	Fetal Stomach	stomach
47	chr17:46205400-46217400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr17:46205600-46207400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr17:46205600-46208400	Weak transcription	Brain Hippocampus Middle	brain
50	chr17:46205600-46209600	Weak transcription	Brain Cingulate Gyrus	brain

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