Variant report

Variant	rs2236953
Chromosome Location	chr3:50424182-50424183
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50398149..50400701-chr3:50422132..50425114,2	MCF-7	breast:
2	chr3:50423026..50425468-chr3:50433598..50435342,2	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1107265	0.94[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.88[EUR][1000 genomes]
rs11130250	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12490042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492113	0.87[CEU][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes]
rs12494849	0.83[CEU][hapmap]
rs13087550	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13091933	0.83[CEU][hapmap]
rs13099869	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1467913	0.83[CEU][hapmap]
rs1467914	0.83[CEU][hapmap]
rs2027854	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2073496	0.88[EUR][1000 genomes]
rs2236950	0.95[MEX][hapmap];0.87[AMR][1000 genomes]
rs2236954	0.94[CEU][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.88[EUR][1000 genomes]
rs2236955	0.94[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2236956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236957	0.94[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs2236958	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236959	0.94[CEU][hapmap];0.86[JPT][hapmap]
rs2236961	1.00[CEU][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2236962	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2236963	1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2236964	0.94[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs2236965	0.94[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs2236967	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2236968	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2236971	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2236973	0.94[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs2236975	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2236979	0.94[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs2236981	0.82[EUR][1000 genomes]
rs2236983	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2236984	0.94[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs2236987	0.94[CEU][hapmap]
rs2236988	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2282752	0.94[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2282753	0.94[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.88[EUR][1000 genomes]
rs2282754	0.94[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.88[EUR][1000 genomes]
rs2282756	1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282758	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2282760	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2298955	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]
rs34762184	0.88[CEU][hapmap]
rs35986136	0.88[CEU][hapmap]
rs4688719	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4688720	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs628081	0.83[CEU][hapmap]
rs6446206	0.85[EUR][1000 genomes]
rs6786523	0.83[CEU][hapmap]
rs6787890	1.00[CEU][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6788459	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6792502	0.83[CEU][hapmap]
rs6807916	0.88[CEU][hapmap]
rs71326932	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs734767	0.94[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.88[EUR][1000 genomes]
rs743756	0.94[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs743757	0.94[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs743857	0.94[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs762895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs762897	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs762898	1.00[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs763030	0.83[CEU][hapmap]
rs8180034	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs916217	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs929047	1.00[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9835537	0.94[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.83[EUR][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2236953	CAMP	cis	cerebellum	SCAN
rs2236953	NCKIPSD	cis	cerebellum	SCAN
rs2236953	APEH	cis	cerebellum	SCAN
rs2236953	CAMKV	cis	parietal	SCAN
rs2236953	AMT	cis	lymphoblastoid	seeQTL
rs2236953	PARP3	cis	parietal	SCAN
rs2236953	HYAL2	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50411400-50430000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:50412800-50428000	Weak transcription	Right Ventricle	heart
3	chr3:50415200-50428400	Weak transcription	Brain Anterior Caudate	brain
4	chr3:50417000-50428000	Weak transcription	Gastric	stomach
5	chr3:50419600-50426200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:50420600-50425200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:50421400-50428000	Weak transcription	Esophagus	oesophagus
8	chr3:50421600-50426800	Weak transcription	Fetal Intestine Small	intestine
9	chr3:50421600-50428200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:50421800-50425600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:50422400-50428000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:50422600-50426800	Enhancers	Fetal Brain Male	brain
13	chr3:50422600-50428000	Weak transcription	Lung	lung
14	chr3:50422800-50426400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:50423200-50424600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:50423200-50427200	Weak transcription	Spleen	Spleen
17	chr3:50423400-50424600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:50423400-50424600	Flanking Active TSS	Brain Germinal Matrix	brain
19	chr3:50423600-50425200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:50423800-50424200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:50423800-50424200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
22	chr3:50423800-50424200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:50423800-50426000	Enhancers	Fetal Brain Female	brain
24	chr3:50424000-50431000	Enhancers	Fetal Muscle Leg	muscle
25	chr3:50424000-50433000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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