Variant report

Variant	rs4468992
Chromosome Location	chr3:160983135-160983136
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160980523..160999163-chr3:161073509..161094838,104	MCF-7	breast:
2	chr3:160977108..160997706-chr3:161077424..161093939,169	MCF-7	breast:
3	chr3:160936882..160947576-chr3:160982516..160994324,28	MCF-7	breast:
4	chr3:160979328..160995719-chr3:161119748..161144811,174	MCF-7	breast:
5	chr3:160982688..160996909-chr3:161122010..161144833,109	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000240567	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1017799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12486069	0.87[ASN][1000 genomes]
rs12486111	0.89[JPT][hapmap]
rs12486998	0.89[JPT][hapmap]
rs12487002	0.90[JPT][hapmap]
rs12488127	0.89[JPT][hapmap]
rs12489004	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12489125	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12490149	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12494725	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12496235	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13315320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13319558	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13319771	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1450518	0.88[JPT][hapmap]
rs16831850	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16831864	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16831882	0.87[ASN][1000 genomes]
rs16831942	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2306209	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28451189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28704960	0.87[ASN][1000 genomes]
rs28713364	0.97[AMR][1000 genomes]
rs3925722	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4296611	0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4352387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4580574	0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4635725	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57903480	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59567999	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59593286	0.83[AMR][1000 genomes]
rs59757775	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59776766	0.87[ASN][1000 genomes]
rs59867530	0.82[AMR][1000 genomes]
rs60121330	0.87[ASN][1000 genomes]
rs6441350	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6441363	0.94[AMR][1000 genomes]
rs6441365	0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6441372	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6441375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6762064	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6771581	0.83[AMR][1000 genomes]
rs6774919	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6775446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6775931	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6778186	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6782415	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6782518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6785714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6787447	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6788738	0.97[AMR][1000 genomes]
rs6790805	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6794601	0.89[JPT][hapmap]
rs6796168	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6801664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6805976	0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73017340	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026933	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73026967	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026968	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026983	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026987	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73878309	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7615833	1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7615868	0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7624791	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7626773	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7634299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7651924	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7652624	0.82[CHB][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9290070	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9290071	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9682249	0.85[AMR][1000 genomes]
rs9810351	0.87[ASN][1000 genomes]
rs9812574	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9818470	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9818835	0.87[ASN][1000 genomes]
rs9818992	0.82[ASN][1000 genomes]
rs9819793	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9822705	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9822916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9823424	0.87[ASN][1000 genomes]
rs9824535	0.87[ASN][1000 genomes]
rs9824805	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9826857	0.87[ASN][1000 genomes]
rs9830183	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9833270	0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9834806	0.94[AMR][1000 genomes]
rs9835530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9838945	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9841871	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9842290	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9847842	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9850455	0.90[JPT][hapmap]
rs9851699	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9855112	0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9855572	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9856742	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9858907	0.87[ASN][1000 genomes]
rs9859641	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9860980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9862867	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9871753	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9872514	0.90[JPT][hapmap]
rs9876077	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9877309	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9884100	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9985364	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160939800-160995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:160941000-160984600	Weak transcription	Small Intestine	intestine
3	chr3:160941000-160993400	Weak transcription	Pancreas	Pancrea
4	chr3:160956400-160993000	Weak transcription	Esophagus	oesophagus
5	chr3:160958600-160983600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:160966200-160983400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:160966200-160987400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:160966200-160993200	Weak transcription	Right Ventricle	heart
9	chr3:160968800-160992200	Weak transcription	Brain Angular Gyrus	brain
10	chr3:160970200-160983800	Weak transcription	NHLF	lung
11	chr3:160970400-160984200	Weak transcription	Hela-S3	cervix
12	chr3:160970400-160995600	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:160970800-160995600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:160971000-160983600	Weak transcription	Thymus	Thymus
15	chr3:160971000-160984200	Weak transcription	Brain Anterior Caudate	brain
16	chr3:160971000-160987400	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:160971000-160989000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:160971000-160993800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:160971000-160995400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:160971000-160995400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:160971200-160984400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:160971200-160988800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:160971200-160995200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:160971200-160996000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:160971800-160993000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:160972200-160996600	Weak transcription	Brain Substantia Nigra	brain
27	chr3:160972400-160993800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr3:160972600-160984400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:160972800-160995400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:160973000-160984000	Weak transcription	Stomach Mucosa	stomach
31	chr3:160973200-160983800	Weak transcription	K562	blood
32	chr3:160973200-160984600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr3:160973200-160993200	Weak transcription	Gastric	stomach
34	chr3:160973400-160989000	Weak transcription	Fetal Thymus	thymus
35	chr3:160974600-160990000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:160975400-160995800	Weak transcription	Fetal Intestine Large	intestine
37	chr3:160976400-160985400	Weak transcription	Fetal Lung	lung
38	chr3:160976400-160989400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr3:160976600-160983400	Weak transcription	HUVEC	blood vessel
40	chr3:160976600-160983800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:160976600-160984200	Weak transcription	Brain Germinal Matrix	brain
42	chr3:160976600-160989200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:160976600-160995400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:160976800-160983600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:160976800-160991800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:160978000-160984800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:160979200-160999800	Weak transcription	Psoas Muscle	Psoas
48	chr3:160980000-160983200	Enhancers	Liver	Liver
49	chr3:160980000-160983800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:160980200-160985200	Enhancers	NHDF-Ad	bronchial

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