Variant report

Variant	rs11065282
Chromosome Location	chr12:121264415-121264416
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121207161..121209960-chr12:121261845..121264886,3	MCF-7	breast:
2	chr12:121262055..121264947-chr12:121269553..121271661,2	K562	blood:
3	chr12:121017642..121019153-chr12:121263056..121265187,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167272	Chromatin interaction
ENSG00000157837	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10774572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10849791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10849807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065264	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11065283	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065284	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065293	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065307	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[EUR][1000 genomes]
rs1151849	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs1151859	0.82[ASN][1000 genomes]
rs1151862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11608262	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11611087	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168944	0.83[ASN][1000 genomes]
rs1168946	0.83[ASN][1000 genomes]
rs1168948	0.83[ASN][1000 genomes]
rs1168953	0.83[ASN][1000 genomes]
rs1177585	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1179939	0.83[ASN][1000 genomes]
rs12371178	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12579868	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12580949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12809299	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12822123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12824150	0.85[CEU][hapmap]
rs12825746	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12831094	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13746	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs1467283	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1542859	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1696357	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs2015462	0.83[ASN][1000 genomes]
rs2047568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2062507	0.85[CEU][hapmap];0.81[MKK][hapmap]
rs2393717	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2461475	0.95[ASN][1000 genomes]
rs2650017	0.83[ASN][1000 genomes]
rs2893876	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3213566	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[ASN][1000 genomes]
rs3213567	0.82[ASN][1000 genomes]
rs3213570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3213572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34009825	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34076777	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35706672	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35905305	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3809313	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3842985	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3861797	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3883901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3897746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3901854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4454799	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs471688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4766979	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766980	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4767935	0.85[CEU][hapmap];0.81[MKK][hapmap]
rs4767937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs487943	0.85[ASN][1000 genomes]
rs494632	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs508595	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs520753	0.91[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs525425	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs531782	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs533264	0.84[ASN][1000 genomes]
rs534415	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs548452	0.85[ASN][1000 genomes]
rs572016	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs577961	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58291418	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58918988	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs590625	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs602984	0.83[ASN][1000 genomes]
rs609700	0.84[ASN][1000 genomes]
rs610694	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs61946382	0.80[EUR][1000 genomes]
rs624216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs625228	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs647881	0.84[ASN][1000 genomes]
rs661647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs665585	0.85[ASN][1000 genomes]
rs666976	0.83[ASN][1000 genomes]
rs7137504	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7305849	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73413868	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73415734	0.81[EUR][1000 genomes]
rs7969140	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs869781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs909053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9431	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.80[ASN][1000 genomes]
rs989986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs989987	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1045178	chr12:121231461-121271734	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11065282	MLEC	cis	lymphoblastoid	seeQTL
rs11065282	WSB2	cis	cerebellum	SCAN
rs11065282	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs11065282	HPD	cis	parietal	SCAN
rs11065282	ACADS	cis	Thyroid	GTEx
rs11065282	P2RX4	cis	cerebellum	SCAN
rs11065282	SPPL3	cis	parietal	SCAN
rs11065282	SPPL3	cis	cerebellum	SCAN
rs11065282	SRRM4	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121222200-121274000	Weak transcription	Lung	lung
2	chr12:121222600-121268600	Weak transcription	Esophagus	oesophagus
3	chr12:121222600-121268600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr12:121248000-121265200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr12:121248200-121267200	Weak transcription	Fetal Stomach	stomach
6	chr12:121248200-121272200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:121248400-121266800	Weak transcription	Fetal Intestine Large	intestine
8	chr12:121248600-121267200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:121248800-121268600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr12:121248800-121270400	Weak transcription	Primary B cells from cord blood	blood
11	chr12:121248800-121271600	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr12:121248800-121271800	Weak transcription	Dnd41	blood
13	chr12:121250800-121266600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr12:121253800-121268600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:121254000-121268600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:121255800-121270000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:121256000-121266200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:121256000-121267200	Weak transcription	Placenta	Placenta
19	chr12:121259600-121265400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:121259800-121264800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:121260200-121268800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:121260400-121270400	Weak transcription	Fetal Muscle Leg	muscle
23	chr12:121260600-121266400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:121260600-121268600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:121260800-121272400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:121261000-121265200	Weak transcription	Ovary	ovary
27	chr12:121261200-121264600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:121261400-121265200	Weak transcription	Gastric	stomach
29	chr12:121261400-121265400	Weak transcription	GM12878-XiMat	blood
30	chr12:121261400-121266600	Weak transcription	Fetal Thymus	thymus
31	chr12:121261400-121268600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:121261400-121269400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:121261600-121264600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:121261600-121264800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:121261600-121264800	Weak transcription	Brain Hippocampus Middle	brain
36	chr12:121261600-121265400	Weak transcription	Brain Substantia Nigra	brain
37	chr12:121261600-121266600	Weak transcription	Brain Anterior Caudate	brain
38	chr12:121261600-121267800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:121261600-121268400	Weak transcription	Fetal Kidney	kidney
40	chr12:121261600-121268600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:121261600-121268600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:121261600-121268600	Weak transcription	Adipose Nuclei	Adipose
43	chr12:121261600-121268600	Weak transcription	Right Atrium	heart
44	chr12:121261600-121268600	Weak transcription	Right Ventricle	heart
45	chr12:121261600-121268800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:121261600-121268800	Weak transcription	Fetal Brain Female	brain
47	chr12:121261600-121268800	Weak transcription	Small Intestine	intestine
48	chr12:121261600-121268800	Weak transcription	Thymus	Thymus
49	chr12:121261600-121269200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr12:121261600-121269200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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