Variant report

Variant	rs35293936
Chromosome Location	chr2:209227348-209227349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10177810	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10182087	0.85[CEU][hapmap]
rs10186350	1.00[YRI][hapmap]
rs10190458	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10206991	0.88[AMR][1000 genomes]
rs10497901	0.82[CEU][hapmap]
rs11538998	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11693993	0.85[EUR][1000 genomes]
rs11885913	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11891163	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895188	1.00[CHD][hapmap]
rs11897777	0.88[AMR][1000 genomes]
rs11902124	0.82[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes]
rs12475932	1.00[CHD][hapmap]
rs1259699	0.82[CEU][hapmap];1.00[CHD][hapmap]
rs1259700	0.82[CEU][hapmap]
rs12694110	0.85[YRI][hapmap]
rs12991283	1.00[CEU][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12998277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13000248	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs13395035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13397965	0.88[AMR][1000 genomes]
rs13400356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407268	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1347664	0.82[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap]
rs1437413	0.82[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap]
rs16841224	0.82[CEU][hapmap];0.88[MEX][hapmap]
rs16841236	1.00[CHD][hapmap];0.88[MEX][hapmap]
rs17699838	1.00[ASN][1000 genomes]
rs17700235	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1816612	0.82[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap]
rs1866046	1.00[CHD][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs1898436	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1898437	0.86[EUR][1000 genomes]
rs28418905	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28885800	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34259292	0.90[AMR][1000 genomes]
rs35217101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856350	0.85[CEU][hapmap]
rs4234089	0.85[CEU][hapmap]
rs4462735	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs4673402	0.85[YRI][hapmap]
rs4675748	0.81[TSI][hapmap]
rs4675761	0.97[EUR][1000 genomes]
rs61193569	0.84[AMR][1000 genomes]
rs6435435	1.00[CHD][hapmap]
rs66826643	1.00[ASN][1000 genomes]
rs6716615	0.82[CEU][hapmap];1.00[CHD][hapmap]
rs6717082	0.82[CEU][hapmap];1.00[CHD][hapmap]
rs6725527	1.00[ASN][1000 genomes]
rs6728530	0.80[YRI][hapmap]
rs67393765	0.84[AMR][1000 genomes]
rs67660353	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67757182	0.84[AMR][1000 genomes]
rs67965883	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72986744	0.84[AMR][1000 genomes]
rs7563597	0.81[AMR][1000 genomes]
rs7583022	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs7608913	0.84[AMR][1000 genomes]
rs959660	0.85[CEU][hapmap]
rs999890	1.00[CHD][hapmap];0.92[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs999891	1.00[CHD][hapmap];0.92[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv875752	chr2:209141066-209235373	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv437315	chr2:209204714-209249613	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35293936	PIKFYVE	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209219400-209228000	Weak transcription	Hela-S3	cervix
2	chr2:209220000-209227600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:209220000-209228000	Weak transcription	NHEK	skin
4	chr2:209220200-209228000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:209220200-209229800	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:209220200-209235200	Weak transcription	K562	blood
7	chr2:209220400-209227400	Weak transcription	Fetal Brain Female	brain
8	chr2:209220400-209227600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:209220400-209227800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:209220400-209227800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:209220400-209227800	Weak transcription	HMEC	breast
12	chr2:209220400-209228000	Weak transcription	Right Ventricle	heart
13	chr2:209220600-209227800	Weak transcription	HSMMtube	muscle
14	chr2:209220600-209227800	Weak transcription	NH-A	brain
15	chr2:209221800-209231200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:209222000-209227400	Weak transcription	NHDF-Ad	bronchial
17	chr2:209222000-209227800	Weak transcription	NHLF	lung
18	chr2:209222000-209228000	Weak transcription	Osteobl	bone
19	chr2:209222200-209228000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:209223600-209227600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:209224000-209227400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:209224200-209227400	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:209224200-209227600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:209224200-209227800	Weak transcription	HSMM	muscle
25	chr2:209224200-209228000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:209224400-209228000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:209224600-209227400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:209224600-209227600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:209224600-209228000	Weak transcription	GM12878-XiMat	blood
30	chr2:209224800-209227400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:209224800-209234200	Weak transcription	Placenta	Placenta
32	chr2:209225200-209227600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr2:209225400-209228200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:209225800-209228600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:209226000-209227800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:209226000-209227800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:209226000-209228000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:209226000-209230200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:209226000-209230800	Weak transcription	Spleen	Spleen
40	chr2:209226000-209234200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:209226200-209228200	Weak transcription	Fetal Intestine Small	intestine
42	chr2:209227200-209227400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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