Variant report

Variant	rs2298955
Chromosome Location	chr3:50431194-50431195
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50420263..50421916-chr3:50428504..50431466,2	K562	blood:
2	chr3:50430686..50433104-chr3:50437469..50439018,2	MCF-7	breast:
3	chr3:50382316..50385000-chr3:50428533..50431219,2	K562	blood:

Variant related genes	Relation type
ENSG00000004838	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1107265	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130250	0.83[AMR][1000 genomes]
rs12490042	0.94[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12492113	0.82[CEU][hapmap];0.84[AMR][1000 genomes]
rs12494849	0.89[CEU][hapmap]
rs13087550	0.94[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1467913	0.89[CEU][hapmap]
rs1467914	0.89[CEU][hapmap];0.87[GIH][hapmap]
rs2027854	0.84[AMR][1000 genomes]
rs2073496	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236950	0.82[MEX][hapmap]
rs2236951	0.87[MEX][hapmap]
rs2236953	0.94[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2236954	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236955	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236956	0.94[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2236957	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236958	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2236959	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2236961	0.94[CEU][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2236962	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2236963	0.94[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2236964	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2236965	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2236967	0.94[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2236968	0.94[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2236971	0.92[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2236973	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2236975	0.94[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2236979	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2236981	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2236983	0.85[AMR][1000 genomes]
rs2236984	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2236987	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2236988	0.94[CEU][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs2282752	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282753	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2282754	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2282756	0.94[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs2282758	0.94[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2282760	0.85[AMR][1000 genomes]
rs2282762	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34762184	0.82[CEU][hapmap]
rs35986136	0.82[CEU][hapmap]
rs4688719	0.94[CEU][hapmap];0.80[AMR][1000 genomes]
rs4688720	0.82[AMR][1000 genomes]
rs6446206	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6786523	0.89[CEU][hapmap];0.87[GIH][hapmap]
rs6787890	0.94[CEU][hapmap];0.86[TSI][hapmap]
rs6788459	0.84[AMR][1000 genomes]
rs6792502	0.89[CEU][hapmap]
rs6807916	0.82[CEU][hapmap]
rs71326932	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs734767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743756	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs743757	1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs743857	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs750510	0.84[CEU][hapmap]
rs762895	0.94[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs762897	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs762898	0.94[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs763030	0.89[CEU][hapmap]
rs8180034	0.80[AMR][1000 genomes]
rs916217	0.94[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs929047	0.94[CEU][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes]
rs9835537	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9867588	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	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
3	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
6	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	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
8	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
9	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' 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	93 gene(s)	inside rSNPs	diseases
10	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
11	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
12	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
13	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
14	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
15	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
16	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
17	nsv876778	chr3:50413707-50465518	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
18	nsv590271	chr3:50420554-50436716	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2298955	ALS2CL	cis	parietal	SCAN
rs2298955	PARP3	cis	parietal	SCAN
rs2298955	APEH	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50424000-50433000	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:50426000-50431400	Enhancers	Brain Germinal Matrix	brain
3	chr3:50426400-50431600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:50426400-50438000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:50426600-50434000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:50428200-50432200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:50428800-50434800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:50429000-50432600	Weak transcription	Fetal Intestine Large	intestine
9	chr3:50429000-50433200	Weak transcription	Adipose Nuclei	Adipose
10	chr3:50429200-50431600	Weak transcription	Fetal Stomach	stomach
11	chr3:50429200-50433400	Weak transcription	Fetal Brain Female	brain
12	chr3:50429400-50432800	Weak transcription	Placenta	Placenta
13	chr3:50429400-50433000	Weak transcription	Fetal Intestine Small	intestine
14	chr3:50429600-50432200	Weak transcription	Brain Angular Gyrus	brain
15	chr3:50429600-50432200	Weak transcription	Pancreas	Pancrea
16	chr3:50429600-50432600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:50429800-50431200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
18	chr3:50429800-50432600	Weak transcription	Spleen	Spleen
19	chr3:50430000-50432800	Weak transcription	Stomach Mucosa	stomach
20	chr3:50430200-50431600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:50430200-50432600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:50430400-50432800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr3:50430800-50431200	Strong transcription	Lung	lung
24	chr3:50430800-50432400	Weak transcription	Right Ventricle	heart
25	chr3:50430800-50434200	Weak transcription	Right Atrium	heart
26	chr3:50431000-50433000	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:50431000-50435400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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