Variant report

Variant	rs3213985
Chromosome Location	chr2:46840735-46840736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46839258..46842242-chr2:46842497..46844194,2	K562	blood:
2	chr2:46694377..46696235-chr2:46839785..46842336,2	MCF-7	breast:
3	chr2:46794873..46797184-chr2:46839917..46841642,2	K562	blood:
4	chr2:46838114..46840779-chr2:46841900..46844194,2	MCF-7	breast:
5	chr2:46838843..46841805-chr2:46843233..46844922,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119878	Chromatin interaction
ENSG00000151665	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1057899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060656	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs11306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1137748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs11901678	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903907	0.87[ASN][1000 genomes]
rs13404342	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13406609	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13410076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1376406	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1456018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035272	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17035361	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs1809087	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2276554	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3768723	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs3768724	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3768725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4300884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4377377	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57134465	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57955462	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58101879	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58342271	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59183773	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59823825	0.87[ASN][1000 genomes]
rs60211996	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60738814	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61252474	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6544904	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544908	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6713104	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];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719813	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6727471	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733143	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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs68104662	0.93[ASN][1000 genomes]
rs72875696	0.87[ASN][1000 genomes]
rs7563577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589908	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591561	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs7592446	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs962467	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9808496	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
9	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3213985	PIGF	cis	lymphoblastoid	seeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46790000-46842000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr2:46796800-46842800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:46797800-46841000	Weak transcription	K562	blood
4	chr2:46802400-46842600	Weak transcription	NHEK	skin
5	chr2:46803400-46842800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:46807600-46842400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:46807600-46842600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:46807800-46842400	Weak transcription	NHLF	lung
9	chr2:46807800-46842600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:46807800-46842800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:46807800-46842800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:46807800-46842800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:46807800-46842800	Weak transcription	HSMMtube	muscle
14	chr2:46807800-46843000	Weak transcription	Brain Germinal Matrix	brain
15	chr2:46807800-46843000	Weak transcription	Fetal Stomach	stomach
16	chr2:46807800-46843200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:46808000-46842800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:46808600-46842800	Weak transcription	Placenta	Placenta
19	chr2:46809400-46842800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:46809600-46842800	Weak transcription	Fetal Thymus	thymus
21	chr2:46810600-46842600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:46811600-46842800	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr2:46811800-46842400	Weak transcription	Osteobl	bone
24	chr2:46811800-46843000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:46812000-46842600	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:46814200-46841600	Weak transcription	Fetal Heart	heart
27	chr2:46819600-46842800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:46819800-46842200	Weak transcription	NHDF-Ad	bronchial
29	chr2:46824200-46842800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:46828000-46842800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:46828600-46842800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:46828600-46842800	Weak transcription	Left Ventricle	heart
33	chr2:46828800-46841600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:46829000-46842800	Weak transcription	Brain Angular Gyrus	brain
35	chr2:46829200-46842600	Weak transcription	Brain Substantia Nigra	brain
36	chr2:46829800-46843200	Weak transcription	Ovary	ovary
37	chr2:46830800-46842400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:46831600-46842800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:46833600-46843200	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:46834000-46841400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:46834200-46841800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr2:46834200-46842600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:46834200-46842800	Weak transcription	Liver	Liver
44	chr2:46834600-46842800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:46834600-46842800	Weak transcription	Right Ventricle	heart
46	chr2:46835200-46842800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:46835400-46842800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:46835800-46843000	Weak transcription	Fetal Brain Male	brain
49	chr2:46836200-46841600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr2:46836400-46842400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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