Variant report

Variant	rs2357263
Chromosome Location	chr2:9846661-9846662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9846347..9848775-chr2:9855960..9857602,2	K562	blood:
2	chr2:9842350..9846952-chr2:9858838..9862900,5	K562	blood:
3	chr2:9843482..9849818-chr2:9850036..9855209,6	K562	blood:
4	chr2:9716130..9717904-chr2:9846619..9848740,2	MCF-7	breast:
5	chr2:9845674..9847302-chr2:9868513..9870809,2	MCF-7	breast:
6	chr2:9830401..9832024-chr2:9844409..9846965,2	K562	blood:
7	chr2:9694686..9696238-chr2:9843890..9846874,2	MCF-7	breast:
8	chr2:9845748..9848155-chr2:9867890..9870403,2	K562	blood:

Variant related genes	Relation type
ENSG00000151694	Chromatin interaction
ENSG00000271855	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10178017	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs10200779	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs10202938	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10929596	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10929597	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10929598	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10929600	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10929602	0.87[EUR][1000 genomes]
rs10929605	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1123269	0.90[CEU][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs11674642	0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11680429	1.00[ASW][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11685771	0.86[MEX][hapmap]
rs11695437	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11892176	0.83[EUR][1000 genomes]
rs11901380	0.83[EUR][1000 genomes]
rs11902412	0.83[EUR][1000 genomes]
rs12466594	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12472594	0.84[EUR][1000 genomes]
rs12475853	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs12476232	0.86[CEU][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap]
rs13024852	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13028425	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs13395171	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs13398163	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs13398193	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs13398304	0.86[CEU][hapmap];0.90[JPT][hapmap]
rs1877953	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2357264	0.91[EUR][1000 genomes]
rs2357265	0.91[EUR][1000 genomes]
rs4459704	0.91[EUR][1000 genomes]
rs4507070	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4668636	0.90[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4668637	0.85[CEU][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4668638	0.87[EUR][1000 genomes]
rs4668639	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4668640	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4669427	0.85[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4669428	0.85[CEU][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4669429	0.86[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4669430	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4669432	0.87[EUR][1000 genomes]
rs4669433	0.88[EUR][1000 genomes]
rs4669435	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4669437	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4669441	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4669445	0.81[CEU][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs5020306	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58961346	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6432033	0.85[CEU][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6724483	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6735280	0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6736421	0.83[EUR][1000 genomes]
rs6738072	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6756567	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs7423455	0.95[JPT][hapmap]
rs7578933	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7592044	0.83[EUR][1000 genomes]
rs7602784	0.95[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7605675	0.95[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs885572	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2357263	HPCAL1	cis	parietal	SCAN
rs2357263	ODC1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9837000-9849600	Weak transcription	Pancreas	Pancrea
2	chr2:9843800-9852000	Weak transcription	Left Ventricle	heart
3	chr2:9844000-9846800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:9844000-9847200	Weak transcription	Fetal Heart	heart
5	chr2:9844000-9847200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:9844200-9847400	Weak transcription	Gastric	stomach
7	chr2:9844200-9852000	Weak transcription	Esophagus	oesophagus
8	chr2:9844400-9848400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:9844400-9848800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:9844400-9848800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:9844400-9849000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr2:9844400-9849600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:9844400-9849600	Weak transcription	HMEC	breast
14	chr2:9844600-9849000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:9844600-9849800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:9844800-9848400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:9845000-9848000	Weak transcription	K562	blood
18	chr2:9845000-9849600	Weak transcription	Spleen	Spleen
19	chr2:9845000-9850000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:9845200-9849800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr2:9845200-9852000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr2:9845400-9847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:9845400-9848000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr2:9845400-9848200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:9845400-9860600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:9845600-9851600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:9846400-9846800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:9846400-9846800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:9846400-9848400	Bivalent Enhancer	HepG2	liver
30	chr2:9846600-9847000	Enhancers	Fetal Brain Female	brain
31	chr2:9846600-9848400	Enhancers	A549	lung

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