Variant report

Variant	rs3766723
Chromosome Location	chr1:185015534-185015535
allele	G/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: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	chr1:185014501..185017888-chr1:185123055..185126846,5	MCF-7	breast:
2	chr1:185012738..185016714-chr1:185123889..185127545,9	K562	blood:
3	chr1:185015280..185017121-chr1:185031346..185033713,2	MCF-7	breast:
4	chr1:185013842..185016800-chr1:185124120..185127493,5	MCF-7	breast:
5	chr1:185014725..185016444-chr1:185285813..185288103,2	K562	blood:
6	chr1:185014175..185016130-chr8:128748218..128750891,2	MCF-7	breast:
7	chr1:185012738..185017820-chr1:185123187..185127311,9	K562	blood:
8	chr1:185014410..185016846-chr1:185107860..185109945,2	K562	blood:
9	chr1:184722993..184726139-chr1:185013897..185016469,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000116679	Chromatin interaction
ENSG00000116406	Chromatin interaction
ENSG00000136997	Chromatin interaction
ENSG00000116668	Chromatin interaction
ENSG00000273004	Chromatin interaction
ENSG00000121486	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1008502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10453829	0.89[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs1046592	1.00[CEU][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10489579	0.89[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs10489581	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10797997	1.00[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs10797998	1.00[CEU][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs10911674	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.99[ASN][1000 genomes]
rs10911676	0.85[EUR][1000 genomes]
rs10911682	0.87[AMR][1000 genomes]
rs12022419	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12023744	0.88[EUR][1000 genomes]
rs12025995	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12026000	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12027607	0.80[EUR][1000 genomes]
rs12028809	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap]
rs12030761	0.93[ASN][1000 genomes]
rs12030778	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12030967	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12031837	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12035073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12035433	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12037466	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12037692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12038919	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs12039541	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12039657	0.93[ASN][1000 genomes]
rs12040650	1.00[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs12041374	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12043427	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12043495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12043561	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12043617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12044161	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs12044997	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12045772	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12046095	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12046202	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12046801	0.85[EUR][1000 genomes]
rs12049293	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12064938	0.80[EUR][1000 genomes]
rs12086086	1.00[CEU][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs12094983	1.00[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs12401293	0.80[EUR][1000 genomes]
rs12404644	1.00[CEU][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes]
rs12408279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12409926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1415072	0.89[CHB][hapmap];0.80[CHD][hapmap]
rs1544052	1.00[CEU][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes]
rs16865296	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2050566	0.89[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs2146328	0.89[CHB][hapmap];0.80[CHD][hapmap]
rs2273881	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2378958	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs3766719	0.81[GIH][hapmap]
rs3766720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3806243	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap]
rs41264588	0.87[AMR][1000 genomes]
rs41264590	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56107433	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61125463	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61495015	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6674490	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs6684586	0.90[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs6698122	0.86[JPT][hapmap]
rs72739677	0.80[EUR][1000 genomes]
rs72739679	0.80[EUR][1000 genomes]
rs72739699	1.00[ASN][1000 genomes]
rs72741807	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72741808	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv525731	chr1:184812165-185038104	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv947340	chr1:185012848-185017415	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
5	esv3421775	chr1:185013354-185016202	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185013600-185016000	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr1:185013600-185016200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:185013800-185015600	Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr1:185013800-185015800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:185013800-185015800	Active TSS	Fetal Lung	lung
6	chr1:185013800-185016200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:185013800-185016200	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr1:185013800-185016600	Active TSS	GM12878-XiMat	blood
9	chr1:185013800-185017000	Active TSS	NHLF	lung
10	chr1:185014000-185015600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
11	chr1:185014000-185015600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:185014000-185015600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:185014000-185015600	Active TSS	Brain Angular Gyrus	brain
14	chr1:185014000-185015600	Active TSS	Brain Cingulate Gyrus	brain
15	chr1:185014000-185015600	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr1:185014000-185015800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:185014000-185015800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:185014000-185015800	Active TSS	Brain Hippocampus Middle	brain
19	chr1:185014000-185015800	Active TSS	Brain Substantia Nigra	brain
20	chr1:185014000-185015800	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr1:185014000-185015800	Active TSS	Right Ventricle	heart
22	chr1:185014000-185016000	Active TSS	Muscle Satellite Cultured Cells	--
23	chr1:185014000-185016000	Active TSS	Colonic Mucosa	Colon
24	chr1:185014000-185016000	Active TSS	Colon Smooth Muscle	Colon
25	chr1:185014000-185016000	Active TSS	Fetal Muscle Trunk	muscle
26	chr1:185014000-185016000	Active TSS	Psoas Muscle	Psoas
27	chr1:185014000-185016000	Active TSS	Rectal Smooth Muscle	rectum
28	chr1:185014000-185016000	Active TSS	Thymus	Thymus
29	chr1:185014000-185016000	Active TSS	HSMM	muscle
30	chr1:185014000-185016000	Active TSS	NHEK	skin
31	chr1:185014000-185016200	Active TSS	Fetal Intestine Large	intestine
32	chr1:185014000-185016200	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr1:185014000-185016200	Active TSS	Stomach Smooth Muscle	stomach
34	chr1:185014000-185016200	Active TSS	HMEC	breast
35	chr1:185014200-185015600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:185014200-185015600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:185014200-185015600	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr1:185014200-185015600	Active TSS	Esophagus	oesophagus
39	chr1:185014200-185015600	Active TSS	Gastric	stomach
40	chr1:185014200-185015600	Active TSS	Lung	lung
41	chr1:185014200-185015600	Active TSS	Pancreas	Pancrea
42	chr1:185014200-185015600	Active TSS	NH-A	brain
43	chr1:185014200-185015800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:185014200-185015800	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr1:185014200-185015800	Active TSS	Aorta	Aorta
46	chr1:185014200-185015800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr1:185014200-185015800	Active TSS	Fetal Heart	heart
48	chr1:185014200-185015800	Active TSS	Fetal Intestine Small	intestine
49	chr1:185014200-185015800	Active TSS	Left Ventricle	heart
50	chr1:185014200-185016000	Active TSS	Fetal Brain Female	brain

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