Variant report

Variant	rs2041572
Chromosome Location	chr17:46205273-46205274
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:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:46125822..46128075-chr17:46204595..46207129,2	MCF-7	breast:
2	chr17:46107614..46109746-chr17:46202771..46206014,3	K562	blood:
3	chr17:46175748..46179895-chr17:46202616..46205569,5	MCF-7	breast:
4	chr17:46174713..46176905-chr17:46204166..46206499,2	MCF-7	breast:
5	chr17:46202062..46204690-chr17:46205157..46208075,2	K562	blood:
6	chr17:46183681..46186136-chr17:46203632..46206520,3	MCF-7	breast:
7	chr17:46103475..46106134-chr17:46203314..46206264,3	MCF-7	breast:
8	chr17:46101075..46105793-chr17:46203518..46208640,6	MCF-7	breast:
9	chr17:46202062..46204213-chr17:46205157..46207474,2	K562	blood:
10	chr17:46123780..46125492-chr17:46204870..46207142,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNX11-6	chr17:46204111-46206694	NONHSAT054385

No data

Variant related genes	Relation type
ENSG00000108468	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000005243	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1002330	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1010228	0.85[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1010230	0.84[ASN][1000 genomes]
rs10445339	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10445377	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10853098	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11079806	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs11079808	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs11079809	0.84[ASN][1000 genomes]
rs11079814	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11651097	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs11870056	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11872095	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12150533	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12452956	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12603115	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12603380	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12936731	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs12941830	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12947089	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12948810	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1316657	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1377201	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1452663	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1452665	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs1452666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1452667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1468270	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs16951519	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs16953941	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs16954268	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs16954324	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs17620033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17681336	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1860862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860863	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860866	0.84[ASN][1000 genomes]
rs1979897	0.86[CHB][hapmap]
rs2021752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2021811	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2051821	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2060876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2072441	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs208005	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs208008	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs208009	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs208015	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2109982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2109983	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2109984	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2123341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2229369	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2240119	0.81[JPT][hapmap]
rs2240120	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2240121	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2240122	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2278868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2305433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2325804	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs2924257	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs2938483	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34949267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3744346	0.86[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs3792692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3792694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3805363	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3805370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3805371	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3897986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3944039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4794447	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4794451	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs4794505	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4794517	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4794525	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55982346	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62066407	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62066447	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6504025	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs6504108	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs67446770	0.83[EUR][1000 genomes]
rs6847	0.87[JPT][hapmap]
rs71356520	0.82[ASN][1000 genomes]
rs7209730	0.84[ASN][1000 genomes]
rs7210149	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7212202	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs7213876	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7217496	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs7219967	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7220619	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7220768	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7220922	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7222136	0.86[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs7223867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7224014	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs7224461	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7225435	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7225550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7225865	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs741058	0.84[ASN][1000 genomes]
rs7501770	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs757353	0.81[JPT][hapmap]
rs758999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065670	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs8066391	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs8069064	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8069263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8071199	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs8071879	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs8072282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8075270	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8077860	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs875065	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs882380	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs954226	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs978263	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs9807087	0.84[ASN][1000 genomes]
rs9899275	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs9899461	0.85[CHB][hapmap];0.87[JPT][hapmap]

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
rs2041572	SNX11	cis	Lymphoblastoid	GTEx

Chromatin state (count:93 , 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	chr17:46192400-46205400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr17:46192800-46205600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr17:46196800-46208800	Weak transcription	K562	blood
6	chr17:46197800-46221000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr17:46199400-46212400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:46199800-46209600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr17:46200200-46206000	Weak transcription	Pancreas	Pancrea
10	chr17:46200400-46236600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr17:46200600-46205800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr17:46200600-46206400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr17:46200600-46209000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr17:46200600-46209600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr17:46200800-46207400	Weak transcription	Right Ventricle	heart
16	chr17:46200800-46208400	Weak transcription	Colon Smooth Muscle	Colon
17	chr17:46200800-46209000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr17:46200800-46212400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr17:46201000-46205400	Weak transcription	Fetal Lung	lung
20	chr17:46201000-46205400	Weak transcription	Left Ventricle	heart
21	chr17:46201000-46206400	Weak transcription	Ovary	ovary
22	chr17:46201000-46206600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr17:46201000-46207600	Weak transcription	Dnd41	blood
24	chr17:46201200-46205600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr17:46201200-46206000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr17:46201200-46207000	Weak transcription	Fetal Intestine Large	intestine
27	chr17:46201200-46208000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr17:46201200-46209600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr17:46201400-46207600	Weak transcription	Fetal Kidney	kidney
30	chr17:46201400-46208400	Weak transcription	Brain Angular Gyrus	brain
31	chr17:46201400-46217600	Weak transcription	Fetal Thymus	thymus
32	chr17:46201600-46205800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr17:46201600-46206400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr17:46201600-46207000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr17:46202800-46205400	Strong transcription	Fetal Stomach	stomach
36	chr17:46203000-46217000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr17:46203200-46205400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr17:46203200-46205600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr17:46203400-46205600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr17:46203400-46205600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr17:46203400-46205800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr17:46203600-46207000	Weak transcription	Colonic Mucosa	Colon
43	chr17:46203800-46205400	Genic enhancers	Brain Germinal Matrix	brain
44	chr17:46203800-46206200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr17:46203800-46209000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr17:46204000-46205800	Enhancers	HUVEC	blood vessel
47	chr17:46204000-46220000	Weak transcription	GM12878-XiMat	blood
48	chr17:46204200-46205400	Enhancers	A549	lung
49	chr17:46204200-46205600	Enhancers	Fetal Muscle Leg	muscle
50	chr17:46204200-46205600	Enhancers	Hela-S3	cervix

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