Variant report

Variant	rs2236968
Chromosome Location	chr3:50465975-50465976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50404490..50407147-chr3:50464074..50466361,2	K562	blood:
2	chr3:50464652..50467495-chr3:50469517..50472085,2	MCF-7	breast:
3	chr3:50459643..50461705-chr3:50463877..50466245,2	MCF-7	breast:
4	chr3:50394585..50396465-chr3:50463450..50466153,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271858	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10510755	1.00[ASW][hapmap]
rs1107265	0.94[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs11130250	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12490042	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12492113	0.87[CEU][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes]
rs12494849	0.83[CEU][hapmap]
rs13087550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13091933	0.83[CEU][hapmap]
rs13099869	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1467913	0.83[CEU][hapmap]
rs1467914	0.83[CEU][hapmap]
rs2027854	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2071803	1.00[ASW][hapmap]
rs2073496	0.86[EUR][1000 genomes]
rs2073498	1.00[ASW][hapmap]
rs2236950	1.00[ASW][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes]
rs2236953	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]
rs2236954	0.94[CEU][hapmap];0.90[GIH][hapmap];0.86[EUR][1000 genomes]
rs2236955	0.94[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2236956	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2236957	0.94[CEU][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs2236958	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2236959	0.94[CEU][hapmap];0.82[JPT][hapmap]
rs2236961	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2236962	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2236963	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2236964	0.94[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs2236965	0.94[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs2236967	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236973	0.94[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2236975	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2236979	0.94[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs2236981	0.87[EUR][1000 genomes]
rs2236983	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2236984	0.94[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs2236987	0.94[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2236988	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2282752	0.94[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs2282753	0.94[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2282754	0.94[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2282756	1.00[ASW][hapmap];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[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2282758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282760	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282762	0.82[EUR][1000 genomes]
rs2298955	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]
rs2301639	1.00[ASW][hapmap]
rs28365992	1.00[ASW][hapmap]
rs34762184	0.88[CEU][hapmap]
rs35986136	0.88[CEU][hapmap]
rs3806708	1.00[ASW][hapmap]
rs4688719	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4688720	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs628081	0.83[CEU][hapmap]
rs6446206	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6786523	0.83[CEU][hapmap]
rs6787890	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6788459	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6792502	0.83[CEU][hapmap]
rs6807916	0.88[CEU][hapmap]
rs71326932	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs734767	0.94[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs743756	0.94[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs743757	0.94[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs743857	0.94[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs762895	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs762897	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs762898	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs763030	0.83[CEU][hapmap]
rs8180034	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs916217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs929047	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9835537	0.94[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs9867588	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
9	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
10	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
11	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
12	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
13	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
15	esv3445182	chr3:50458687-50496660	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2236968	APEH	cis	cerebellum	SCAN
rs2236968	NCKIPSD	cis	cerebellum	SCAN
rs2236968	TRAIP	cis	parietal	SCAN
rs2236968	PARP3	cis	parietal	SCAN
rs2236968	CAMKV	cis	parietal	SCAN
rs2236968	HYAL2	cis	parietal	SCAN
rs2236968	CAMP	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50445600-50471400	Weak transcription	Spleen	Spleen
2	chr3:50450600-50471000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:50459400-50470200	Enhancers	Brain Germinal Matrix	brain
4	chr3:50460200-50467400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:50461600-50467400	Weak transcription	Brain Anterior Caudate	brain
6	chr3:50462200-50471400	Weak transcription	Gastric	stomach
7	chr3:50462600-50467600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:50463000-50467600	Weak transcription	Lung	lung
9	chr3:50463200-50467800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:50464200-50470400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr3:50464400-50466000	Bivalent Enhancer	Fetal Brain Male	brain
12	chr3:50464600-50469800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr3:50464800-50466200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
14	chr3:50465200-50466200	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr3:50465400-50466200	Bivalent Enhancer	Fetal Brain Female	brain
16	chr3:50465400-50472600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:50465600-50466200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:50465600-50467400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:50465600-50467800	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:50465600-50468400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:50465600-50485800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:50465800-50466000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:50465800-50466000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:50465800-50466200	Enhancers	Right Atrium	heart
25	chr3:50465800-50472200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:50465800-50487000	Weak transcription	Fetal Intestine Small	intestine

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