Variant report

Variant	rs17035361
Chromosome Location	chr2:46823032-46823033
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46821971..46824630-chr2:46842972..46846352,3	MCF-7	breast:
2	chr2:46822981..46825273-chr2:46839295..46841308,2	K562	blood:
3	chr2:46768347..46770630-chr2:46822894..46825695,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119878	Chromatin interaction
ENSG00000250565	Chromatin interaction
ENSG00000151665	Chromatin interaction
ENSG00000119729	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1057899	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1060656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11306	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1137748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901678	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11903907	0.87[ASN][1000 genomes]
rs13404342	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13406609	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13410076	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1376406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1456018	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17035272	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1809087	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2276554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3213985	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs3768723	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768724	0.93[ASN][1000 genomes]
rs3768725	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4300884	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4377377	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57134465	1.00[ASN][1000 genomes]
rs57955462	1.00[ASN][1000 genomes]
rs58101879	1.00[ASN][1000 genomes]
rs58342271	0.94[ASN][1000 genomes]
rs59183773	1.00[ASN][1000 genomes]
rs59823825	0.87[ASN][1000 genomes]
rs60211996	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60738814	0.94[ASN][1000 genomes]
rs61252474	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544904	1.00[ASN][1000 genomes]
rs6544908	0.85[ASN][1000 genomes]
rs6713104	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6719813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727471	1.00[ASN][1000 genomes]
rs6733143	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6756134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68104662	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72875696	0.87[ASN][1000 genomes]
rs7563577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs7589908	1.00[ASN][1000 genomes]
rs7591561	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7592446	0.94[ASN][1000 genomes]
rs962467	0.87[ASN][1000 genomes]
rs9808496	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	esv3440660	chr2:46817659-46823480	Weak transcription Strong transcription	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	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
10	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17035361	PIGF	cis	lymphoblastoid	seeQTL
rs17035361	CRIPT	cis	lymphoblastoid	seeQTL
rs17035361	ATP6V1E2	cis	multi-tissue	Pritchard

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46783600-46838000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr2:46790000-46842000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr2:46796800-46838000	Weak transcription	Fetal Kidney	kidney
4	chr2:46796800-46842800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:46797800-46841000	Weak transcription	K562	blood
6	chr2:46798200-46838000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:46802400-46842600	Weak transcription	NHEK	skin
8	chr2:46802800-46837000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:46803400-46842800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:46805600-46836400	Weak transcription	HSMM	muscle
11	chr2:46807600-46828400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:46807600-46842400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:46807600-46842600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:46807800-46824600	Weak transcription	Fetal Intestine Small	intestine
15	chr2:46807800-46825000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:46807800-46828400	Weak transcription	Brain Substantia Nigra	brain
17	chr2:46807800-46835200	Weak transcription	Fetal Intestine Large	intestine
18	chr2:46807800-46835200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:46807800-46835400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:46807800-46835400	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:46807800-46836400	Weak transcription	Primary T cells from cord blood	blood
22	chr2:46807800-46842400	Weak transcription	NHLF	lung
23	chr2:46807800-46842600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:46807800-46842800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:46807800-46842800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:46807800-46842800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:46807800-46842800	Weak transcription	HSMMtube	muscle
28	chr2:46807800-46843000	Weak transcription	Brain Germinal Matrix	brain
29	chr2:46807800-46843000	Weak transcription	Fetal Stomach	stomach
30	chr2:46807800-46843200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:46808000-46824200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:46808000-46836000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:46808000-46836400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:46808000-46838000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:46808000-46842800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:46808200-46836800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr2:46808200-46838400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:46808600-46842800	Weak transcription	Placenta	Placenta
39	chr2:46809400-46842800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:46809600-46842800	Weak transcription	Fetal Thymus	thymus
41	chr2:46810600-46842600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:46811000-46835200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:46811200-46835800	Weak transcription	Primary B cells from cord blood	blood
44	chr2:46811600-46842800	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr2:46811800-46836200	Weak transcription	Adipose Nuclei	Adipose
46	chr2:46811800-46842400	Weak transcription	Osteobl	bone
47	chr2:46811800-46843000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:46812000-46828400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:46812000-46828400	Weak transcription	GM12878-XiMat	blood
50	chr2:46812000-46842600	Weak transcription	Brain Hippocampus Middle	brain

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