Variant report

Variant	rs440299
Chromosome Location	chr12:120220282-120220283
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	chr12:120133826..120135360-chr12:120217778..120220518,2	MCF-7	breast:
2	chr12:120119419..120120944-chr12:120218866..120221340,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10459141	0.92[EUR][1000 genomes]
rs11064906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11064911	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11064919	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12300601	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12302281	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs1318272	0.83[MEX][hapmap]
rs169408	0.94[EUR][1000 genomes]
rs203331	0.96[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs203332	1.00[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs203335	0.90[EUR][1000 genomes]
rs203339	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs203352	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs203361	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs203364	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs203366	0.88[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs203368	1.00[CEU][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2074052	0.83[MEX][hapmap]
rs2240309	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240310	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2952444	0.83[MEX][hapmap]
rs369180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847957	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs385844	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3858710	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs385930	0.96[CEU][hapmap];0.83[CHB][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs385959	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs386259	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[EUR][1000 genomes]
rs386928	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393773	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs394155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs400551	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407464	1.00[CEU][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs407692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413236	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432718	0.81[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.88[LWK][hapmap];0.96[MKK][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs433091	0.81[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4462403	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4766948	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4766949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767843	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4767844	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs574142	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs574155	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs679381	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs679773	0.88[EUR][1000 genomes]
rs7133437	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7136729	0.90[EUR][1000 genomes]
rs7300010	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7953072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967982	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7969405	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs804716	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804717	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs440299	LRRC43	cis	parietal	SCAN
rs440299	FBXW8	cis	cerebellum	SCAN
rs440299	DYNLL1	cis	parietal	SCAN
rs440299	PXN	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120149400-120224800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:120156600-120221400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:120184200-120224600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr12:120185400-120227200	Strong transcription	Dnd41	blood
5	chr12:120188000-120228800	Weak transcription	HSMMtube	muscle
6	chr12:120189400-120225600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:120190000-120244800	Weak transcription	Primary B cells from cord blood	blood
8	chr12:120190200-120226400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:120191200-120235600	Weak transcription	Colonic Mucosa	Colon
10	chr12:120195600-120223000	Weak transcription	Spleen	Spleen
11	chr12:120197200-120223200	Weak transcription	Gastric	stomach
12	chr12:120199200-120241000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:120203600-120222400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:120204000-120224800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:120205200-120222200	Weak transcription	Esophagus	oesophagus
16	chr12:120207000-120224000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:120208400-120220800	Weak transcription	NH-A	brain
18	chr12:120208600-120226600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:120209400-120293600	Weak transcription	Primary T cells from cord blood	blood
20	chr12:120209600-120220600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:120209800-120220400	Weak transcription	HepG2	liver
22	chr12:120209800-120220400	Weak transcription	HSMM	muscle
23	chr12:120209800-120221200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:120209800-120221400	Weak transcription	Brain Germinal Matrix	brain
25	chr12:120210000-120221200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:120210000-120223000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr12:120210000-120228800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr12:120210000-120235400	Weak transcription	Brain Angular Gyrus	brain
29	chr12:120210000-120239200	Weak transcription	Fetal Brain Female	brain
30	chr12:120210600-120221800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:120210600-120226600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:120210800-120221400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:120210800-120231400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr12:120213800-120226800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:120214600-120220600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:120214600-120220800	Weak transcription	K562	blood
37	chr12:120214600-120241000	Weak transcription	Fetal Intestine Large	intestine
38	chr12:120214800-120220600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:120214800-120221400	Weak transcription	Fetal Muscle Leg	muscle
40	chr12:120215600-120224600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:120217200-120224800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr12:120217400-120223200	Strong transcription	Fetal Thymus	thymus
43	chr12:120217400-120225200	Strong transcription	Thymus	Thymus
44	chr12:120217800-120224600	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr12:120217800-120228600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:120218200-120224400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:120218800-120220400	Genic enhancers	GM12878-XiMat	blood
48	chr12:120218800-120220600	Weak transcription	NHLF	lung
49	chr12:120218800-120221400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:120218800-120224600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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