Variant report

Variant	rs2269935
Chromosome Location	chr12:48516464-48516465
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr12:48516236-48516483	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48515800..48518794-chr12:48562400..48565355,2	K562	blood:
2	chr12:48513033..48514796-chr12:48515513..48517416,2	MCF-7	breast:
3	chr12:48498567..48501846-chr12:48512929..48518601,8	MCF-7	breast:
4	chr12:48511276..48513909-chr12:48515822..48517335,2	K562	blood:

Variant related genes	Relation type
PFKM	TF binding region
ENSG00000257885	Chromatin interaction
ENSG00000152556	Chromatin interaction
ENSG00000079387	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10082861	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10219623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10219645	0.89[ASN][1000 genomes]
rs10467101	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs10875724	0.93[JPT][hapmap]
rs10875725	1.00[JPT][hapmap]
rs10875731	0.82[EUR][1000 genomes]
rs10875732	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs10875735	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10875736	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10875737	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10875738	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10875740	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10875745	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10875746	0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875747	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875748	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875750	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875756	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875762	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10875767	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs10875770	0.89[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs10875772	0.89[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap]
rs10875792	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10875793	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs11168355	0.84[GIH][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs11168357	0.93[JPT][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs11168369	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs11168370	0.80[EUR][1000 genomes]
rs11168371	0.93[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs11168374	0.82[EUR][1000 genomes]
rs11168383	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11168386	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11168401	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11168403	0.85[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11168413	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11168414	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168415	0.97[ASN][1000 genomes]
rs11168416	0.97[ASN][1000 genomes]
rs11168418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168420	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168421	0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11168422	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168425	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11168427	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168433	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168450	0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs11168459	0.89[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs11168516	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11558768	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12228854	0.82[YRI][hapmap]
rs12296244	0.82[EUR][1000 genomes]
rs12297004	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12297470	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12301339	0.89[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12304476	0.84[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12305182	0.93[JPT][hapmap]
rs12305511	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs12305647	0.83[EUR][1000 genomes]
rs12306290	0.94[ASN][1000 genomes]
rs12306451	0.84[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12310813	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12310999	0.82[EUR][1000 genomes]
rs12311774	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12311953	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12312134	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs12313300	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12313404	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12315625	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17122620	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17122666	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17122812	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs1859445	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2012773	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2079295	0.93[JPT][hapmap]
rs2107638	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2158516	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2228500	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269933	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2269936	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2279464	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs2286021	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3782910	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3782911	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3809322	0.82[YRI][hapmap]
rs4760609	0.84[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs4760619	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4760622	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs4760680	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4760681	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760684	0.97[ASN][1000 genomes]
rs4760687	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4760689	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760690	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760695	0.84[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs4760696	0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4760697	0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs58952582	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60106007	0.97[ASN][1000 genomes]
rs60761335	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61343568	0.91[ASN][1000 genomes]
rs61918774	0.82[EUR][1000 genomes]
rs61918806	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61918809	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61918810	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6580659	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7135779	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs719008	0.93[JPT][hapmap]
rs725454	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7299135	0.93[JPT][hapmap]
rs7299271	0.93[JPT][hapmap]
rs73102065	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73102067	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7485355	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7486424	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs886588	0.84[ASW][hapmap];0.93[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9634261	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs989144	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]

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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2269935	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs2269935	PRKAG1	cis	parietal	SCAN
rs2269935	AQP6	cis	parietal	SCAN
rs2269935	FAM186B	cis	parietal	SCAN
rs2269935	RP1-228P16.1	cis	Heart Left Ventricle	GTEx
rs2269935	ASB8	cis	parietal	SCAN
rs2269935	SENP1	cis	parietal	SCAN
rs2269935	ASB8	cis	cerebellum	SCAN
rs2269935	RP1-228P16.1	cis	Thyroid	GTEx
rs2269935	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2269935	RP1-228P16.1	cis	Artery Tibial	GTEx
rs2269935	H1FNT	cis	cerebellum	SCAN
rs2269935	LOC255411	cis	cerebellum	SCAN
rs2269935	SENP1	cis	cerebellum	SCAN

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	chr12:48513800-48516600	Weak transcription	Fetal Thymus	thymus
6	chr12:48513800-48519400	Weak transcription	Primary T cells from cord blood	blood
7	chr12:48513800-48524400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr12:48513800-48525000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:48513800-48525000	Weak transcription	Lung	lung
10	chr12:48513800-48525800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:48513800-48526000	Weak transcription	Colonic Mucosa	Colon
12	chr12:48513800-48526400	Weak transcription	Gastric	stomach
13	chr12:48513800-48526600	Weak transcription	Thymus	Thymus
14	chr12:48513800-48526800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:48514000-48516800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:48514000-48516800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:48514000-48518600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:48514000-48520200	Weak transcription	Fetal Lung	lung
19	chr12:48514000-48520600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr12:48514000-48521200	Weak transcription	Primary B cells from cord blood	blood
21	chr12:48514000-48522000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:48514000-48522200	Weak transcription	Adipose Nuclei	Adipose
23	chr12:48514000-48523200	Weak transcription	Fetal Kidney	kidney
24	chr12:48514000-48524200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr12:48514000-48524200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:48514000-48524600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr12:48514000-48525000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:48514000-48525000	Weak transcription	Brain Substantia Nigra	brain
29	chr12:48514000-48525000	Weak transcription	Esophagus	oesophagus
30	chr12:48514000-48525600	Weak transcription	Placenta	Placenta
31	chr12:48514000-48526400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr12:48514000-48526600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:48514000-48526600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:48514000-48536600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr12:48514000-48537200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:48514200-48516600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:48514200-48516600	Weak transcription	Colon Smooth Muscle	Colon
38	chr12:48514200-48517200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:48514200-48518200	Weak transcription	A549	lung
40	chr12:48514200-48523200	Weak transcription	HSMMtube	muscle
41	chr12:48514200-48527000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:48514400-48516600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:48514400-48516600	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr12:48514400-48516800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:48514400-48516800	Weak transcription	Osteobl	bone
46	chr12:48514400-48518000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr12:48514400-48518200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr12:48514400-48518400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr12:48514400-48519400	Weak transcription	Aorta	Aorta
50	chr12:48514400-48523200	Weak transcription	Rectal Smooth Muscle	rectum

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