Variant report

Variant	rs168245
Chromosome Location	chr3:156405931-156405932
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156401581..156406675-chr3:156542145..156546248,5	MCF-7	breast:
2	chr3:156390425..156393975-chr3:156403365..156406512,4	K562	blood:
3	chr3:156342470..156344204-chr3:156404618..156406838,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197980	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs11710516	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1355280	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1397194	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1397195	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1510269	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1510270	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs168295	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171077	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs180746	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs180747	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs182935	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs182936	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs184677	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1858229	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs186928	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs193423	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2054881	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2129909	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2136691	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2136692	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs237245	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs237246	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2665390	0.95[ASN][1000 genomes]
rs343991	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343995	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343996	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343997	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343998	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344000	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs344001	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs344005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344006	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344008	0.95[ASN][1000 genomes]
rs344009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344013	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344015	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344016	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs344017	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344023	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344029	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs344032	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344047	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344048	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344049	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344050	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344052	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344053	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344054	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344055	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344058	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344059	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344060	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344061	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs344062	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344063	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs344064	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344065	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344066	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344068	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344069	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344070	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs345987	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs419287	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs427384	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4279048	0.94[ASN][1000 genomes]
rs4429586	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4679784	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680297	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4680298	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4680299	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5012666	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6441089	0.83[AMR][1000 genomes]
rs6441092	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6441093	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6441094	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6441095	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6799457	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7640593	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs871232	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs871233	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs907063	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs931990	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs978108	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs978109	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9823112	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9833951	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9877043	0.83[AMR][1000 genomes];0.96[EUR][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	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS 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	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156394000-156436000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:156394200-156412600	Weak transcription	Placenta	Placenta
3	chr3:156394400-156411800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:156395600-156438600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:156395800-156408600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:156396200-156407400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:156396400-156407400	Weak transcription	Esophagus	oesophagus
8	chr3:156396400-156407400	Weak transcription	Spleen	Spleen
9	chr3:156396400-156408800	Weak transcription	Colonic Mucosa	Colon
10	chr3:156396400-156413000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:156396400-156414400	Weak transcription	Thymus	Thymus
12	chr3:156396400-156424800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:156396600-156441000	Weak transcription	Lung	lung
14	chr3:156397800-156413000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:156398400-156408800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr3:156398600-156409600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:156399200-156407400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:156399200-156407400	Weak transcription	Fetal Intestine Large	intestine
19	chr3:156399200-156412400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:156399600-156407400	Weak transcription	Fetal Brain Female	brain
21	chr3:156399800-156407400	Weak transcription	Gastric	stomach
22	chr3:156399800-156408600	Genic enhancers	NHEK	skin
23	chr3:156399800-156410200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:156399800-156411200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:156399800-156411400	Weak transcription	Fetal Thymus	thymus
26	chr3:156399800-156411800	Enhancers	Brain Hippocampus Middle	brain
27	chr3:156399800-156413200	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:156400000-156412200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:156400400-156411600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:156401200-156406400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr3:156401600-156409400	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr3:156402200-156406600	Enhancers	Stomach Mucosa	stomach
33	chr3:156402600-156407400	Weak transcription	Right Atrium	heart
34	chr3:156402600-156410800	Enhancers	Liver	Liver
35	chr3:156402800-156409400	Enhancers	Fetal Heart	heart
36	chr3:156403000-156406000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
37	chr3:156403000-156406800	Enhancers	HUVEC	blood vessel
38	chr3:156403400-156407400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:156403400-156409200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:156403400-156421800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr3:156403600-156408000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:156403600-156409200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:156403600-156412000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:156403800-156406200	Weak transcription	Fetal Brain Male	brain
45	chr3:156403800-156406600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr3:156403800-156407400	Weak transcription	Pancreas	Pancrea
47	chr3:156403800-156407400	Weak transcription	Right Ventricle	heart
48	chr3:156403800-156408400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:156403800-156408800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:156403800-156409600	Genic enhancers	HMEC	breast

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