Variant report

Variant	rs2292814
Chromosome Location	chr2:172586567-172586568
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172585756..172589058-chr2:172589522..172592081,3	MCF-7	breast:
2	chr2:172585739..172588158-chr2:172595691..172597501,2	K562	blood:

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10179020	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10184770	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10185633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191399	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10196521	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10201520	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1022358	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10930493	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10930497	1.00[CEU][hapmap]
rs1105264	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11677573	0.89[ASW][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs11678892	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11887208	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11903123	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12464262	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12467010	0.81[EUR][1000 genomes]
rs12471160	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12478189	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12479374	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12617265	0.89[ASW][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12619137	0.89[ASW][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12692971	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12692979	1.00[JPT][hapmap]
rs13012103	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13017988	0.89[ASW][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13399316	0.81[EUR][1000 genomes]
rs1400816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1515812	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1517678	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1543168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1554165	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1607253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16859721	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17580984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17614989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17615013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1850031	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1878583	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1996425	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2037164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2056202	0.89[ASW][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2176466	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2292813	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2357064	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2357206	0.89[ASW][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2357207	0.81[EUR][1000 genomes]
rs2357208	0.81[EUR][1000 genomes]
rs28372952	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs312915	0.84[AFR][1000 genomes]
rs312917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3770444	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770453	0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs3770457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3821094	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821095	0.83[YRI][hapmap]
rs3821096	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4507064	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4668417	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58565148	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59414074	0.95[AFR][1000 genomes]
rs60706248	0.81[EUR][1000 genomes]
rs61588295	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6433313	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433315	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433317	0.89[ASW][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6433318	0.81[EUR][1000 genomes]
rs6711813	0.89[ASW][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6736159	0.89[ASW][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6742905	0.83[EUR][1000 genomes]
rs6753859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs6758494	1.00[JPT][hapmap]
rs6760680	1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7340516	0.89[ASW][hapmap];1.00[JPT][hapmap]
rs7574090	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7574711	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7580132	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7580232	0.89[ASW][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7588025	0.83[ASW][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs7588351	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7594478	0.88[ASW][hapmap];1.00[JPT][hapmap]
rs7597525	0.81[EUR][1000 genomes]
rs925881	0.89[ASW][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9287948	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];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs949548	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9636293	0.83[AFR][1000 genomes]
rs970948	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[YRI][hapmap];0.88[ASN][1000 genomes]
rs979956	0.80[AFR][1000 genomes]
rs979957	0.80[AFR][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	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv522519	chr2:172586567-172600310	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2292814	LASS6	cis	parietal	SCAN
rs2292814	DYNC1I2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172545200-172611200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:172545400-172588000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:172545800-172588000	Weak transcription	Right Ventricle	heart
4	chr2:172546600-172602800	Weak transcription	Small Intestine	intestine
5	chr2:172552200-172587600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:172554400-172588000	Weak transcription	Esophagus	oesophagus
7	chr2:172559600-172605200	Weak transcription	Colonic Mucosa	Colon
8	chr2:172561200-172587800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:172561400-172601800	Weak transcription	Fetal Heart	heart
10	chr2:172564200-172610000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr2:172569000-172618600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:172569800-172611400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:172571400-172597800	Strong transcription	HSMM	muscle
14	chr2:172571800-172594200	Strong transcription	HUVEC	blood vessel
15	chr2:172572000-172595400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:172574800-172587800	Weak transcription	Lung	lung
17	chr2:172575400-172595600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:172579800-172589200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:172579800-172595600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:172579800-172611200	Strong transcription	Adipose Nuclei	Adipose
21	chr2:172580000-172598000	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr2:172580200-172588200	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr2:172580200-172589600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr2:172580200-172590000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:172580200-172595400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr2:172580200-172595400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr2:172580200-172595600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:172580200-172596000	Strong transcription	Primary hematopoietic stem cells	blood
29	chr2:172580200-172611200	Strong transcription	Placenta	Placenta
30	chr2:172580400-172589600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr2:172580400-172595400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:172580400-172595600	Strong transcription	Primary T cells from cord blood	blood
33	chr2:172580400-172610600	Strong transcription	Fetal Thymus	thymus
34	chr2:172580400-172611400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:172580400-172611400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:172580600-172595400	Strong transcription	Primary B cells from cord blood	blood
37	chr2:172580800-172587800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
38	chr2:172580800-172595600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr2:172581000-172595000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:172581000-172595400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:172581200-172587600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:172581200-172587600	Weak transcription	Fetal Stomach	stomach
43	chr2:172581200-172587800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:172581200-172587800	Weak transcription	Gastric	stomach
45	chr2:172581200-172587800	Weak transcription	Spleen	Spleen
46	chr2:172581200-172588000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:172581200-172588000	Weak transcription	Aorta	Aorta
48	chr2:172581200-172588000	Weak transcription	Fetal Intestine Small	intestine
49	chr2:172581200-172588000	Weak transcription	Pancreas	Pancrea
50	chr2:172581200-172589800	Strong transcription	Primary T helper cells PMA-I stimulated	--

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