Variant report

Variant	rs11168459
Chromosome Location	chr12:48596241-48596242
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	chr12:48591422..48593721-chr12:48594349..48596928,3	MCF-7	breast:
2	chr12:48418539..48420191-chr12:48595608..48598283,2	K562	blood:

Variant related genes	Relation type
ENSG00000269514	Chromatin interaction
ENSG00000257955	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10082861	0.92[JPT][hapmap]
rs1021313	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10219623	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs10431526	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10437919	0.96[ASN][1000 genomes]
rs10437920	0.96[ASN][1000 genomes]
rs10467101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783234	0.87[ASN][1000 genomes]
rs10875724	0.85[JPT][hapmap]
rs10875725	0.93[JPT][hapmap]
rs10875732	0.92[JPT][hapmap]
rs10875735	0.83[CEU][hapmap]
rs10875745	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs10875746	0.84[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs10875750	0.89[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs10875756	0.81[ASN][1000 genomes]
rs10875762	0.90[ASN][1000 genomes]
rs10875764	0.86[ASN][1000 genomes]
rs10875767	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];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875768	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875769	0.92[ASN][1000 genomes]
rs10875770	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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875777	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875778	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875779	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875782	0.93[ASN][1000 genomes]
rs10875792	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs10875793	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs11168357	0.86[JPT][hapmap]
rs11168369	0.93[JPT][hapmap]
rs11168371	0.93[JPT][hapmap]
rs11168403	0.93[JPT][hapmap]
rs11168413	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs11168414	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs11168418	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs11168420	0.84[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs11168421	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs11168425	0.84[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs11168427	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs11168433	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs11168450	0.84[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs11168483	0.93[ASN][1000 genomes]
rs11168487	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168493	0.88[ASN][1000 genomes]
rs11168508	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168510	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168514	0.89[ASN][1000 genomes]
rs11168516	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs11558768	0.89[ASN][1000 genomes]
rs12227601	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12297470	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs12300647	0.93[ASN][1000 genomes]
rs12301339	0.89[CEU][hapmap]
rs12304476	0.93[JPT][hapmap]
rs12305182	0.86[JPT][hapmap]
rs12305511	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs12305647	0.92[ASN][1000 genomes]
rs12306451	0.93[JPT][hapmap]
rs12310813	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs12312134	0.89[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12317751	0.96[ASN][1000 genomes]
rs12318705	0.93[ASN][1000 genomes]
rs1471997	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap]
rs17122666	0.83[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs17122812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859445	0.94[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs2012773	0.84[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs2054903	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs2079295	0.86[JPT][hapmap]
rs2107638	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2171642	0.93[ASN][1000 genomes]
rs2228500	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs2269933	0.84[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap]
rs2269935	0.89[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs2269936	0.93[JPT][hapmap]
rs2279464	0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2409005	0.90[ASN][1000 genomes]
rs2634675	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs2732439	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs2732465	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs2898065	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2898066	0.91[ASN][1000 genomes]
rs3185921	0.86[CEU][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap]
rs3751273	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap]
rs3782910	0.93[JPT][hapmap]
rs4760609	0.86[JPT][hapmap]
rs4760619	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs4760622	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs4760625	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760681	0.89[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap]
rs4760687	0.84[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs4760689	0.81[ASN][1000 genomes]
rs4760690	0.81[ASN][1000 genomes]
rs4760695	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs4760696	0.84[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4760697	0.84[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4760699	0.88[ASN][1000 genomes]
rs61940962	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61941003	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61941006	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580659	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs7135779	0.83[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs716553	0.96[ASN][1000 genomes]
rs719008	0.86[JPT][hapmap]
rs725454	0.83[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs7297298	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7299135	0.86[JPT][hapmap]
rs7299271	0.86[JPT][hapmap]
rs7302466	0.93[ASN][1000 genomes]
rs7303055	0.96[ASN][1000 genomes]
rs7486008	0.96[ASN][1000 genomes]
rs7486424	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs7975956	0.93[ASN][1000 genomes]
rs8804	0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs886588	0.93[JPT][hapmap]
rs9634261	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs989144	0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv976031	chr12:48594968-48610975	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv976038	chr12:48596152-48610975	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11168459	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs11168459	FAM186B	cis	parietal	SCAN
rs11168459	RND1	cis	cerebellum	SCAN
rs11168459	PFKM	cis	parietal	SCAN
rs11168459	ZNF641	cis	cerebellum	SCAN
rs11168459	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11168459	H1FNT	cis	cerebellum	SCAN
rs11168459	RP1-228P16.1	cis	Thyroid	GTEx
rs11168459	IRAK4	cis	parietal	SCAN
rs11168459	ASB8	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48592800-48600400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:48593000-48596600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:48593200-48596800	Weak transcription	Brain Substantia Nigra	brain
4	chr12:48593200-48599000	Weak transcription	Brain Angular Gyrus	brain
5	chr12:48593200-48600200	Weak transcription	Right Ventricle	heart
6	chr12:48593400-48600800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:48593600-48596600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:48593800-48596400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:48593800-48596600	Weak transcription	Left Ventricle	heart
10	chr12:48593800-48598400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr12:48593800-48598400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:48594000-48596800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr12:48594000-48598400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:48594200-48596400	Weak transcription	Fetal Kidney	kidney
15	chr12:48594200-48598600	Weak transcription	Colon Smooth Muscle	Colon
16	chr12:48594200-48598800	Weak transcription	Fetal Heart	heart
17	chr12:48594400-48596800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
18	chr12:48594600-48596600	Weak transcription	Right Atrium	heart
19	chr12:48594600-48596800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr12:48594800-48599000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:48595000-48598400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:48595000-48598400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:48595200-48597600	Weak transcription	Brain Anterior Caudate	brain
24	chr12:48595200-48598600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr12:48595200-48598600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:48595200-48598800	Weak transcription	Fetal Lung	lung
27	chr12:48595200-48600400	Weak transcription	Psoas Muscle	Psoas
28	chr12:48595600-48596600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr12:48595600-48609600	Weak transcription	Placenta	Placenta
30	chr12:48595800-48596400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr12:48595800-48596600	Weak transcription	Primary T cells from cord blood	blood
32	chr12:48595800-48599600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:48595800-48600800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:48596000-48596400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
35	chr12:48596000-48596600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
36	chr12:48596000-48596600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
37	chr12:48596000-48596800	ZNF genes & repeats	Fetal Intestine Small	intestine
38	chr12:48596000-48597000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
39	chr12:48596000-48597000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:48596000-48597000	Enhancers	Lung	lung
41	chr12:48596000-48597200	ZNF genes & repeats	Gastric	stomach
42	chr12:48596000-48599600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:48596200-48596600	Weak transcription	Ovary	ovary
44	chr12:48596200-48598400	Weak transcription	Monocytes-CD14+_RO01746	blood

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