Variant report

Variant	rs3103178
Chromosome Location	chr1:92755943-92755944
allele	C/T
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	POLR2A	chr1:92755781-92756025	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:92753480..92757055-chr1:92763323..92765725,4	K562	blood:

Variant related genes	Relation type
GLMN	TF binding region
ENSG00000174842	Chromatin interaction
ENSG00000122484	Chromatin interaction

Extended variants
information (count: 158 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs10159094	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10747503	0.80[ASN][1000 genomes]
rs10875204	1.00[CHD][hapmap]
rs10875209	1.00[JPT][hapmap]
rs10875214	1.00[JPT][hapmap]
rs10875319	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875349	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164226	0.90[ASN][1000 genomes]
rs11164288	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];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164312	0.90[ASN][1000 genomes]
rs11164349	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11164546	0.90[ASN][1000 genomes]
rs11166141	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11166144	1.00[JPT][hapmap]
rs1157470	1.00[JPT][hapmap]
rs11577572	1.00[JPT][hapmap]
rs11577839	0.90[ASN][1000 genomes]
rs11578012	0.90[ASN][1000 genomes]
rs11578400	0.90[ASN][1000 genomes]
rs11585255	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11586989	0.80[ASN][1000 genomes]
rs11588044	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11588153	1.00[JPT][hapmap]
rs11589858	1.00[JPT][hapmap];0.87[LWK][hapmap];0.84[YRI][hapmap];0.90[ASN][1000 genomes]
rs11803457	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024731	0.90[ASN][1000 genomes]
rs12086394	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094293	0.90[ASN][1000 genomes]
rs12119246	1.00[JPT][hapmap]
rs1226183	1.00[JPT][hapmap]
rs1226187	1.00[JPT][hapmap]
rs12401372	0.90[ASN][1000 genomes]
rs12404806	1.00[JPT][hapmap]
rs12407622	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12727665	0.90[ASN][1000 genomes]
rs12729867	1.00[JPT][hapmap]
rs12731923	0.90[ASN][1000 genomes]
rs12735898	0.90[ASN][1000 genomes]
rs12740246	1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[ASN][1000 genomes]
rs12755781	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12757533	1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[ASN][1000 genomes]
rs1325435	0.84[EUR][1000 genomes]
rs1483022	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1487536	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1487540	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1542685	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17519972	1.00[JPT][hapmap]
rs1809606	0.90[ASN][1000 genomes]
rs1872007	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1982720	1.00[JPT][hapmap]
rs2004814	0.90[ASN][1000 genomes]
rs2046620	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2087194	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2093879	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2128645	1.00[JPT][hapmap]
rs2128646	1.00[JPT][hapmap]
rs2391114	1.00[JPT][hapmap]
rs2391158	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2391161	0.92[EUR][1000 genomes]
rs2391162	0.90[ASN][1000 genomes]
rs2839877	1.00[JPT][hapmap]
rs2893200	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3103170	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3103176	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3103181	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3118137	0.80[ASN][1000 genomes]
rs3122321	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3122323	0.81[EUR][1000 genomes]
rs3122325	0.80[EUR][1000 genomes]
rs3122327	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3131813	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131814	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131820	0.92[CEU][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs3131827	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131828	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34090353	0.90[ASN][1000 genomes]
rs35580949	0.90[ASN][1000 genomes]
rs3851271	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3851272	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3851273	1.00[JPT][hapmap]
rs3929737	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4393167	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4414050	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4437922	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4658128	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4658290	1.00[JPT][hapmap]
rs4658294	1.00[JPT][hapmap]
rs4658298	1.00[JPT][hapmap]
rs4658299	1.00[JPT][hapmap]
rs4658300	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488849	1.00[JPT][hapmap]
rs490800	1.00[JPT][hapmap]
rs492164	1.00[JPT][hapmap]
rs493595	1.00[JPT][hapmap]
rs4949888	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4970699	0.90[ASN][1000 genomes]
rs4970713	0.90[ASN][1000 genomes]
rs504606	1.00[JPT][hapmap]
rs506375	1.00[JPT][hapmap]
rs507452	1.00[JPT][hapmap]
rs511546	1.00[JPT][hapmap]
rs515280	1.00[JPT][hapmap]
rs519932	1.00[JPT][hapmap]
rs527412	1.00[JPT][hapmap]
rs529135	1.00[JPT][hapmap]
rs534547	1.00[JPT][hapmap]
rs547699	1.00[JPT][hapmap]
rs553861	1.00[JPT][hapmap]
rs556980	1.00[JPT][hapmap]
rs563113	1.00[JPT][hapmap]
rs563606	1.00[JPT][hapmap]
rs569593	1.00[JPT][hapmap]
rs570368	1.00[JPT][hapmap]
rs573044	1.00[JPT][hapmap]
rs575805	1.00[JPT][hapmap]
rs6603962	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603971	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6604080	1.00[JPT][hapmap]
rs6604082	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6604088	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604090	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661384	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662379	0.90[ASN][1000 genomes]
rs6663114	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6663118	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6663278	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663905	0.90[ASN][1000 genomes]
rs6668803	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];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684317	1.00[JPT][hapmap]
rs6689366	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6692287	0.90[EUR][1000 genomes]
rs6702267	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72720457	0.90[ASN][1000 genomes]
rs733012	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745793	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517541	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518974	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520275	0.96[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524120	0.90[ASN][1000 genomes]
rs7533077	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7539757	0.90[ASN][1000 genomes]
rs7542358	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7542373	1.00[JPT][hapmap]
rs7543947	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545076	1.00[JPT][hapmap]
rs7550680	0.90[ASN][1000 genomes]
rs912794	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9439911	0.90[ASN][1000 genomes]
rs9440085	0.92[EUR][1000 genomes]
rs981583	1.00[JPT][hapmap]
rs9943178	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv871508	chr1:92478130-92781579	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv830592	chr1:92669282-92805629	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv870667	chr1:92697188-92813741	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92707200-92764000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:92709000-92762800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:92710600-92762000	Weak transcription	Fetal Brain Male	brain
4	chr1:92710600-92763400	Weak transcription	Brain Angular Gyrus	brain
5	chr1:92710600-92764000	Weak transcription	Gastric	stomach
6	chr1:92711000-92763600	Weak transcription	HSMMtube	muscle
7	chr1:92711200-92761600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:92711200-92764000	Weak transcription	Spleen	Spleen
9	chr1:92719400-92764000	Weak transcription	Pancreas	Pancrea
10	chr1:92719600-92760800	Weak transcription	Fetal Heart	heart
11	chr1:92720000-92763800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:92722400-92763400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:92723000-92763800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:92724000-92760600	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:92724600-92763800	Weak transcription	Brain Substantia Nigra	brain
16	chr1:92725800-92764000	Weak transcription	Colonic Mucosa	Colon
17	chr1:92727000-92763800	Weak transcription	Right Ventricle	heart
18	chr1:92727200-92759200	Weak transcription	A549	lung
19	chr1:92727200-92763800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:92729800-92763800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:92732000-92763600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:92736000-92763600	Weak transcription	Liver	Liver
23	chr1:92736800-92763800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:92737800-92759400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr1:92738000-92760600	Weak transcription	Hela-S3	cervix
26	chr1:92738000-92763800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:92738400-92763800	Weak transcription	Brain Anterior Caudate	brain
28	chr1:92738800-92763400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:92743200-92759200	Weak transcription	NHLF	lung
30	chr1:92743200-92759600	Weak transcription	Osteobl	bone
31	chr1:92743200-92763600	Weak transcription	NHDF-Ad	bronchial
32	chr1:92744000-92764000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:92745600-92764000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:92745800-92760200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:92745800-92763800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:92745800-92763800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:92745800-92764000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:92745800-92764000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:92746000-92761800	Weak transcription	Esophagus	oesophagus
40	chr1:92746000-92763600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:92746000-92763800	Weak transcription	Aorta	Aorta
42	chr1:92746000-92763800	Weak transcription	Fetal Intestine Small	intestine
43	chr1:92746000-92764000	Weak transcription	Lung	lung
44	chr1:92746400-92762400	Weak transcription	Fetal Brain Female	brain
45	chr1:92748800-92757000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:92750200-92756400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:92750800-92756800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:92750800-92756800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:92750800-92756800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:92750800-92756800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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