Variant report

Variant	rs201198
Chromosome Location	chr3:50636111-50636112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50626963..50632967-chr3:50633102..50640850,17	K562	blood:
2	chr3:50599337..50613537-chr3:50634306..50660129,118	MCF-7	breast:
3	chr3:50613663..50623986-chr3:50635558..50652363,41	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114735	Chromatin interaction
ENSG00000088543	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1034405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs107457	0.88[LWK][hapmap]
rs11130252	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130255	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs11710858	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs11719998	0.85[EUR][1000 genomes]
rs12491425	0.86[EUR][1000 genomes]
rs12639126	0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs129310	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs13075377	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs13076850	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13083004	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084476	0.93[EUR][1000 genomes]
rs13091933	0.94[CEU][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs13094336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094785	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes]
rs13095920	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs13096264	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1458386	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs1458387	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1463496	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1463497	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs175634	0.94[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs17787569	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];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824280	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs201193	0.86[EUR][1000 genomes]
rs201194	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs201196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs201197	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2125366	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2125369	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2168866	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs2199050	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2227280	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232248	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2232253	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2262810	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2269505	1.00[CEU][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs2269507	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355321	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355323	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2608988	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2609001	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2609006	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs2609024	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2609036	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2675772	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2675773	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs2675806	0.90[MEX][hapmap];0.86[TSI][hapmap]
rs2675810	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs2675812	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2675816	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2883652	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs34202063	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34267788	0.89[EUR][1000 genomes]
rs34399912	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34434811	0.89[EUR][1000 genomes]
rs34584636	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];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34756253	0.93[EUR][1000 genomes]
rs34762184	0.89[CHD][hapmap]
rs34889917	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35655236	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35690191	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35714264	0.94[EUR][1000 genomes]
rs35864641	0.89[EUR][1000 genomes]
rs375544	0.86[TSI][hapmap]
rs3792328	0.86[TSI][hapmap]
rs3804627	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs3804628	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs391620	0.85[EUR][1000 genomes]
rs396302	0.86[TSI][hapmap]
rs398703	0.86[EUR][1000 genomes]
rs399484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399971	0.89[EUR][1000 genomes]
rs414171	0.81[EUR][1000 genomes]
rs417592	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs441516	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4429624	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs443030	0.90[EUR][1000 genomes]
rs4482663	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs4533647	0.89[EUR][1000 genomes]
rs453570	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs4688702	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs490634	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59949730	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622502	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs628081	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs6446210	0.82[AMR][1000 genomes]
rs6446214	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs67425923	0.84[EUR][1000 genomes]
rs67588094	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768300	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6775012	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6778680	0.82[CEU][hapmap]
rs6779819	0.86[TSI][hapmap]
rs67813889	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784166	0.94[EUR][1000 genomes]
rs6787521	1.00[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6791880	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs6796769	0.86[TSI][hapmap]
rs695170	0.91[EUR][1000 genomes]
rs71326937	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73082948	0.87[EUR][1000 genomes]
rs750453	0.85[EUR][1000 genomes]
rs750510	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs7611428	0.88[ASW][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs7615703	0.86[TSI][hapmap]
rs7629253	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7646236	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs7650574	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7652260	0.82[EUR][1000 genomes]
rs7652715	0.88[ASW][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap]
rs809451	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs809454	0.87[EUR][1000 genomes]
rs813243	0.86[TSI][hapmap]
rs936405	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs936406	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs9830920	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9838283	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs9839684	1.00[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active 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 target site	55 gene(s)	inside rSNPs	diseases
4	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs201198	NA	cis	multi-tissue	Pritchard
rs201198	CAMP	cis	cerebellum	SCAN
rs201198		cis	Lymphoblastoid	GTEx
rs201198	MAPKAPK3	cis	multi-tissue	Pritchard
rs201198	APEH	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50608200-50637400	Weak transcription	Fetal Kidney	kidney
2	chr3:50623000-50636600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:50628600-50638200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:50628800-50637200	Weak transcription	A549	lung
5	chr3:50628800-50637400	Weak transcription	Brain Substantia Nigra	brain
6	chr3:50629000-50637600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:50630400-50636600	Weak transcription	Ovary	ovary
8	chr3:50630400-50637200	Weak transcription	NHDF-Ad	bronchial
9	chr3:50630600-50636600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:50630600-50636800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:50630600-50637200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:50630600-50637400	Weak transcription	Stomach Mucosa	stomach
13	chr3:50630800-50636200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:50630800-50636400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:50630800-50636400	Weak transcription	Fetal Stomach	stomach
16	chr3:50630800-50636600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:50630800-50636800	Weak transcription	Gastric	stomach
18	chr3:50630800-50637000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:50631000-50636600	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:50631000-50637000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:50631800-50636600	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr3:50632000-50636600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr3:50632000-50636800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:50632200-50636400	Weak transcription	Pancreas	Pancrea
25	chr3:50632200-50636400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:50632200-50636600	Weak transcription	Left Ventricle	heart
27	chr3:50632200-50637400	Weak transcription	Psoas Muscle	Psoas
28	chr3:50632400-50636200	Weak transcription	Liver	Liver
29	chr3:50632400-50636400	Weak transcription	Fetal Heart	heart
30	chr3:50632800-50636800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:50633800-50636400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:50633800-50637000	Weak transcription	Primary T cells from cord blood	blood
33	chr3:50634600-50636800	Weak transcription	Fetal Intestine Small	intestine
34	chr3:50635200-50637400	Enhancers	Dnd41	blood
35	chr3:50635400-50637400	Enhancers	K562	blood
36	chr3:50635400-50637800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:50635600-50636200	Enhancers	Rectal Smooth Muscle	rectum
38	chr3:50635600-50636400	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr3:50635600-50638800	Enhancers	Colon Smooth Muscle	Colon
40	chr3:50635800-50636200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:50635800-50637600	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr3:50635800-50638000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:50635800-50638200	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr3:50635800-50638200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:50635800-50638200	Enhancers	HepG2	liver
46	chr3:50635800-50638600	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr3:50635800-50640400	Enhancers	Placenta	Placenta
48	chr3:50636000-50636400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:50636000-50637000	Weak transcription	Fetal Lung	lung
50	chr3:50636000-50637600	Enhancers	Primary T helper cells PMA-I stimulated	--

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