Variant report

Variant	rs6782518
Chromosome Location	chr3:160938385-160938386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:160938327-160939653	MCF-7	breast:	n/a	n/a
2	ARID3A	chr3:160938277-160939204	HepG2	liver:	n/a	n/a
3	HCFC1	chr3:160938368-160940220	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:160938314-160938412	MCF-7	breast:	n/a	n/a
5	BRCA1	chr3:160938330-160939923	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:160938290-160940780	MCF10A-Er-Src	breast:	n/a	n/a
7	HCFC1	chr3:160938348-160939476	K562	blood:	n/a	n/a
8	POLR2A	chr3:160938088-160940002	GM12891	blood:	n/a	n/a
9	TBL1XR1	chr3:160938236-160939202	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:160938217-160939966	GM12878	blood:	n/a	n/a
11	REST	chr3:160938299-160939835	H1-neurons	neurons:	n/a	chr3:160939420-160939433
12	POLR2A	chr3:160938251-160940135	IMR90	lung:	n/a	n/a
13	POLR2A	chr3:160938308-160940061	MCF10A-Er-Src	breast:	n/a	n/a
14	CHD1	chr3:160938248-160941179	IMR90	lung:	n/a	n/a
15	POLR2A	chr3:160938253-160940262	Hela-S3	cervix:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160937993..160941056-chr3:161047965..161051023,3	MCF-7	breast:
2	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
3	chr3:160938091..160940577-chr7:104653089..104654973,2	MCF-7	breast:
4	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
5	chr12:123319135..123321319-chr3:160936978..160939441,2	MCF-7	breast:
6	chr3:160936897..160938534-chr3:161143997..161146053,2	MCF-7	breast:
7	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
8	chr3:160919833..160921562-chr3:160936344..160938437,2	K562	blood:
9	chr3:160816932..160819441-chr3:160937058..160940131,3	MCF-7	breast:
10	chr3:160938062..160938917-chr4:54930258..54930848,2	Hela-S3	cervix:
11	chr3:160821182..160827138-chr3:160937374..160941314,7	MCF-7	breast:

No data

Variant related genes	Relation type
NMD3	TF binding region
ENSG00000196542	Chromatin interaction
ENSG00000239569	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000243838	Chromatin interaction
ENSG00000109220	Chromatin interaction
ENSG00000240567	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000005483	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1017799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12486069	0.87[ASN][1000 genomes]
rs12486111	1.00[GIH][hapmap];0.89[JPT][hapmap]
rs12486998	1.00[GIH][hapmap];0.89[JPT][hapmap]
rs12487002	0.89[JPT][hapmap]
rs12488127	1.00[GIH][hapmap];0.89[JPT][hapmap]
rs12489004	1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12494725	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12496235	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13315320	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13319558	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13319771	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1450518	0.88[JPT][hapmap]
rs16831799	0.85[AMR][1000 genomes]
rs16831850	1.00[GIH][hapmap];0.91[MEX][hapmap];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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28451189	0.84[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	0.88[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4352387	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4468992	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]
rs4580574	0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4635725	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57903480	0.82[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	1.00[GIH][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6441363	0.94[AMR][1000 genomes]
rs6441365	0.88[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6441372	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6441375	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6762064	0.83[ASW][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6771581	0.83[AMR][1000 genomes]
rs6774919	0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6775446	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6775931	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6778186	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6782415	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6785714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6787447	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6788738	0.97[AMR][1000 genomes]
rs6790805	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6794601	0.89[JPT][hapmap]
rs6796168	0.84[MEX][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6801664	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6805976	0.88[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73017340	0.84[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	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026983	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026987	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026989	0.84[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];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7615868	0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7624791	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7626773	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[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];0.89[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];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7652624	0.82[CHB][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9290070	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9290071	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9682249	0.85[AMR][1000 genomes]
rs9810351	0.87[ASN][1000 genomes]
rs9812574	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9818470	0.91[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];0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9822705	1.00[CHB][hapmap];0.88[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];0.90[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];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9826857	1.00[GIH][hapmap];0.87[ASN][1000 genomes]
rs9830183	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9833270	1.00[GIH][hapmap];0.88[JPT][hapmap];0.84[MEX][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];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9838945	0.88[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	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9847842	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9850455	0.89[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	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9856742	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];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9860980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9862867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9871753	1.00[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9872514	0.89[JPT][hapmap]
rs9876077	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9877309	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]
rs9880536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9884100	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9985364	0.85[AFR][1000 genomes];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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160926000-160938400	Weak transcription	Brain Substantia Nigra	brain
2	chr3:160931000-160938600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:160931800-160938400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:160933200-160939000	Weak transcription	Gastric	stomach
5	chr3:160933400-160938600	Weak transcription	Stomach Mucosa	stomach
6	chr3:160933600-160938400	Weak transcription	Fetal Intestine Large	intestine
7	chr3:160935600-160938400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:160935800-160938400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:160935800-160938600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:160936000-160938400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:160936000-160938600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:160937000-160938400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:160937400-160938800	Weak transcription	Aorta	Aorta
14	chr3:160938000-160938400	Enhancers	Brain Germinal Matrix	brain
15	chr3:160938000-160938400	Enhancers	Hela-S3	cervix
16	chr3:160938000-160938600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr3:160938000-160938600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr3:160938000-160940400	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr3:160938200-160938400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:160938200-160938400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:160938200-160938400	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr3:160938200-160938400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:160938200-160938400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:160938200-160938400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:160938200-160938400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr3:160938200-160938400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:160938200-160938400	Enhancers	Adipose Nuclei	Adipose
28	chr3:160938200-160938400	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr3:160938200-160938400	Enhancers	Fetal Brain Male	brain
30	chr3:160938200-160938400	Enhancers	Fetal Muscle Leg	muscle
31	chr3:160938200-160938400	Enhancers	HepG2	liver
32	chr3:160938200-160938400	Active TSS	NHEK	skin
33	chr3:160938200-160938400	Enhancers	Osteobl	bone
34	chr3:160938200-160938600	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr3:160938200-160938600	Enhancers	Primary B cells from peripheral blood	blood
36	chr3:160938200-160938600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:160938200-160938600	Enhancers	Liver	Liver
38	chr3:160938200-160938600	Enhancers	Brain Anterior Caudate	brain
39	chr3:160938200-160938600	Enhancers	Fetal Lung	lung
40	chr3:160938200-160938600	Enhancers	Fetal Stomach	stomach
41	chr3:160938200-160938600	Enhancers	NHDF-Ad	bronchial
42	chr3:160938200-160938800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr3:160938200-160938800	Flanking Active TSS	Colon Smooth Muscle	Colon
44	chr3:160938200-160938800	Enhancers	Small Intestine	intestine
45	chr3:160938200-160938800	Flanking Active TSS	Dnd41	blood
46	chr3:160938200-160938800	Flanking Active TSS	K562	blood
47	chr3:160938200-160940400	Active TSS	A549	lung
48	chr3:160938200-160940600	Active TSS	Brain Cingulate Gyrus	brain
49	chr3:160938200-160940600	Active TSS	Brain Hippocampus Middle	brain
50	chr3:160938200-160940600	Active TSS	Right Atrium	heart

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