Variant report

Variant	rs11168421
Chromosome Location	chr12:48518333-48518334
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48515800..48518794-chr12:48562400..48565355,2	K562	blood:
2	chr12:48498208..48500662-chr12:48518314..48520006,2	K562	blood:
3	chr12:48503405..48506326-chr12:48517186..48520007,2	K562	blood:
4	chr12:48498567..48501846-chr12:48512929..48518601,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079387	Chromatin interaction
ENSG00000257885	Chromatin interaction
ENSG00000152556	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10082861	1.00[CEU][hapmap];0.94[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]
rs10219623	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10219645	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10467101	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs10875724	0.93[JPT][hapmap]
rs10875725	0.86[ASW][hapmap];0.83[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap]
rs10875732	1.00[JPT][hapmap]
rs10875745	0.87[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875746	0.89[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10875747	0.96[ASN][1000 genomes]
rs10875748	0.96[ASN][1000 genomes]
rs10875750	0.94[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10875756	0.86[ASN][1000 genomes]
rs10875767	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs10875770	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs10875772	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs10875792	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10875793	0.92[JPT][hapmap]
rs11168355	0.84[GIH][hapmap]
rs11168357	0.88[GIH][hapmap];0.93[JPT][hapmap]
rs11168369	1.00[JPT][hapmap]
rs11168371	0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs11168403	1.00[JPT][hapmap]
rs11168413	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168414	0.94[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11168415	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168416	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168418	0.94[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11168420	0.89[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11168422	0.96[ASN][1000 genomes]
rs11168425	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168427	0.94[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11168433	0.94[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11168450	0.89[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs11168459	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs11168516	0.87[JPT][hapmap]
rs12297470	0.91[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12304476	0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs12305182	0.93[JPT][hapmap]
rs12305511	0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs12306290	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12306451	0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs12310813	0.91[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12312134	0.91[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17122666	0.89[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17122812	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs1859445	0.91[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012773	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2079295	0.93[JPT][hapmap]
rs2107638	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2228500	0.94[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2269933	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2269935	0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2269936	1.00[JPT][hapmap]
rs2279464	0.87[JPT][hapmap]
rs2286021	0.94[ASN][1000 genomes]
rs3782910	1.00[JPT][hapmap]
rs4760609	0.84[GIH][hapmap];0.93[JPT][hapmap]
rs4760619	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4760622	0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4760681	0.94[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4760684	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4760689	0.86[ASN][1000 genomes]
rs4760690	0.86[ASN][1000 genomes]
rs4760695	0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4760696	0.89[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs4760697	0.89[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs60106007	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61343568	0.93[ASN][1000 genomes]
rs6580659	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7135779	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs719008	0.93[JPT][hapmap]
rs725454	0.89[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7299135	0.93[JPT][hapmap]
rs7299271	0.93[JPT][hapmap]
rs7485355	0.94[ASN][1000 genomes]
rs7486424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7964359	0.81[CHB][hapmap]
rs8804	0.94[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs886588	0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs9634261	0.87[JPT][hapmap]
rs989144	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11168421	C12orf41	cis	parietal	SCAN
rs11168421	RP1-228P16.1	cis	Thyroid	GTEx
rs11168421	AQP6	cis	parietal	SCAN
rs11168421	RPAP3	cis	cerebellum	SCAN
rs11168421	SENP1	cis	parietal	SCAN
rs11168421	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11168421	FAM186B	cis	parietal	SCAN
rs11168421	RP1-228P16.1	cis	Artery Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48513400-48524800	Weak transcription	Liver	Liver
2	chr12:48513400-48526600	Weak transcription	Spleen	Spleen
3	chr12:48513600-48526400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:48513600-48527000	Weak transcription	Pancreas	Pancrea
5	chr12:48513800-48519400	Weak transcription	Primary T cells from cord blood	blood
6	chr12:48513800-48524400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr12:48513800-48525000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:48513800-48525000	Weak transcription	Lung	lung
9	chr12:48513800-48525800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:48513800-48526000	Weak transcription	Colonic Mucosa	Colon
11	chr12:48513800-48526400	Weak transcription	Gastric	stomach
12	chr12:48513800-48526600	Weak transcription	Thymus	Thymus
13	chr12:48513800-48526800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:48514000-48518600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:48514000-48520200	Weak transcription	Fetal Lung	lung
16	chr12:48514000-48520600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr12:48514000-48521200	Weak transcription	Primary B cells from cord blood	blood
18	chr12:48514000-48522000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr12:48514000-48522200	Weak transcription	Adipose Nuclei	Adipose
20	chr12:48514000-48523200	Weak transcription	Fetal Kidney	kidney
21	chr12:48514000-48524200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr12:48514000-48524200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:48514000-48524600	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr12:48514000-48525000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:48514000-48525000	Weak transcription	Brain Substantia Nigra	brain
26	chr12:48514000-48525000	Weak transcription	Esophagus	oesophagus
27	chr12:48514000-48525600	Weak transcription	Placenta	Placenta
28	chr12:48514000-48526400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:48514000-48526600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:48514000-48526600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:48514000-48536600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr12:48514000-48537200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr12:48514200-48523200	Weak transcription	HSMMtube	muscle
34	chr12:48514200-48527000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:48514400-48518400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr12:48514400-48519400	Weak transcription	Aorta	Aorta
37	chr12:48514400-48523200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:48514400-48525400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr12:48514400-48526400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:48514600-48519800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:48514600-48520000	Weak transcription	NHEK	skin
42	chr12:48514600-48526200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:48514800-48526000	Weak transcription	Brain Hippocampus Middle	brain
44	chr12:48515200-48523400	Weak transcription	Dnd41	blood
45	chr12:48515400-48522200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr12:48515600-48535600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr12:48515800-48519000	Strong transcription	HSMM	muscle
48	chr12:48515800-48522000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr12:48515800-48522400	Strong transcription	NHDF-Ad	bronchial
50	chr12:48515800-48535600	Strong transcription	HUES48 Cell Line	embryonic stem cell

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