Variant report

Variant	rs3201448
Chromosome Location	chr2:86732524-86732525
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	chr2:86730870..86733454-chr2:86738287..86740838,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115561	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1015117	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];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169746	0.81[ASN][1000 genomes]
rs10180036	0.93[CEU][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs10184879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10187880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1020306	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1080551	0.81[ASN][1000 genomes]
rs11127045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11127046	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11127047	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs1137684	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676576	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11684230	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689330	0.81[ASN][1000 genomes]
rs12328637	0.81[EUR][1000 genomes]
rs12613282	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs12614447	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12615285	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];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12623509	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs12714184	0.80[EUR][1000 genomes]
rs12714186	0.96[CEU][hapmap];0.83[GIH][hapmap];0.80[LWK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs12714188	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12714190	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs12714198	0.86[ASW][hapmap];0.96[CEU][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs12714199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12987172	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[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12991654	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13015620	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];0.83[EUR][1000 genomes]
rs13034615	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13390713	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13408041	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13429696	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1465813	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1518807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1629293	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs2241803	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2292887	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2367574	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs308902	0.91[GIH][hapmap]
rs308903	0.89[GIH][hapmap]
rs308910	0.93[GIH][hapmap];0.82[TSI][hapmap]
rs308914	0.95[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs308915	0.87[GIH][hapmap]
rs34666164	0.81[ASN][1000 genomes]
rs3731812	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755002	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];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770058	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs422240	0.94[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap]
rs4832040	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4832041	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4832042	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4832296	0.84[ASN][1000 genomes]
rs4832297	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4832299	0.85[EUR][1000 genomes]
rs4832300	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];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4832302	0.81[ASN][1000 genomes]
rs4832304	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs62147239	0.80[ASN][1000 genomes]
rs6725080	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6738663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6750226	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];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6752371	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs7369138	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557796	0.88[CHB][hapmap];0.81[GIH][hapmap]
rs7568840	0.88[CHB][hapmap]
rs7570640	0.81[ASN][1000 genomes]
rs7584882	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap]
rs7593151	0.84[ASN][1000 genomes]
rs7596717	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs7601115	0.81[EUR][1000 genomes]
rs8179729	0.84[ASN][1000 genomes]
rs9284788	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];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs958561	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs9789777	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3201448	MAT2A	cis	parietal	SCAN
rs3201448	POLR1A	cis	cerebellum	SCAN
rs3201448	VPS24	cis	lymphoblastoid	seeQTL
rs3201448	RNF103	cis	cerebellum	SCAN
rs3201448	VPS24	cis	parietal	SCAN
rs3201448	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs3201448	PTCD3	cis	cerebellum	SCAN
rs3201448	C2orf68	cis	cerebellum	SCAN
rs3201448	IMMT	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:86709200-86737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:86719800-86734600	Weak transcription	Psoas Muscle	Psoas
4	chr2:86724600-86737800	Strong transcription	Stomach Smooth Muscle	stomach
5	chr2:86725400-86733200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:86726400-86735400	Weak transcription	NHLF	lung
7	chr2:86726400-86737400	Weak transcription	HUVEC	blood vessel
8	chr2:86726400-86741800	Weak transcription	NH-A	brain
9	chr2:86726400-86753000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:86726600-86736400	Weak transcription	NHDF-Ad	bronchial
11	chr2:86726600-86748600	Weak transcription	Hela-S3	cervix
12	chr2:86726800-86739000	Weak transcription	K562	blood
13	chr2:86727000-86737200	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr2:86727400-86734400	Weak transcription	Fetal Heart	heart
15	chr2:86727600-86732600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:86727600-86734600	Weak transcription	HMEC	breast
17	chr2:86728000-86732600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:86728000-86734200	Weak transcription	HSMM	muscle
19	chr2:86728000-86737600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:86728000-86737600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:86728000-86737600	Strong transcription	Adipose Nuclei	Adipose
22	chr2:86728000-86737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:86728000-86737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:86728000-86737800	Strong transcription	Fetal Intestine Large	intestine
25	chr2:86728000-86738000	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:86728000-86738400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:86728200-86737800	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:86728200-86737800	Weak transcription	Stomach Mucosa	stomach
29	chr2:86728200-86738400	Strong transcription	Dnd41	blood
30	chr2:86728200-86755800	Weak transcription	Fetal Brain Male	brain
31	chr2:86728400-86736200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:86728400-86737800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:86728400-86738000	Strong transcription	Liver	Liver
34	chr2:86728400-86738400	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr2:86728400-86738400	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:86728400-86738400	Strong transcription	A549	lung
37	chr2:86728400-86747200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:86728600-86737600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:86728600-86738200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:86728600-86738800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr2:86728800-86737400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:86728800-86737800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr2:86728800-86737800	Strong transcription	Placenta	Placenta
44	chr2:86729000-86734800	Weak transcription	Right Ventricle	heart
45	chr2:86729000-86736400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:86729000-86737400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:86729000-86737800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr2:86729000-86738000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr2:86729000-86738000	Strong transcription	Thymus	Thymus
50	chr2:86729000-86738200	Strong transcription	Fetal Muscle Trunk	muscle

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