Variant report

Variant	rs1966272
Chromosome Location	chr2:95926154-95926155
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	chr2:95924662..95927422-chr2:95957580..95961049,3	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10195614	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1104775	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11164122	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs11897976	0.90[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs12992066	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1559483	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs17119148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes]
rs1862897	0.90[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs1875402	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2001254	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2010533	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2042477	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs2098768	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2113417	0.90[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs2320339	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2320619	0.82[EUR][1000 genomes]
rs2320620	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs2320621	0.94[EUR][1000 genomes]
rs2320624	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3105100	0.83[EUR][1000 genomes]
rs3105101	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs3105102	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3105104	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3105105	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3112221	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3112222	0.85[EUR][1000 genomes]
rs3112223	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3112225	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3112228	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3112229	0.85[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs3112230	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3112231	0.88[EUR][1000 genomes]
rs3112984	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3112985	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs3112986	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[EUR][1000 genomes]
rs3112987	0.83[EUR][1000 genomes]
rs3112995	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3112996	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3112997	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3112999	0.92[EUR][1000 genomes]
rs3113000	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3113001	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3755519	0.82[EUR][1000 genomes]
rs3755520	0.86[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs3755521	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs3755523	0.86[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs3755525	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs3772031	0.90[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs3772032	0.90[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs3772033	0.90[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs3772037	0.82[EUR][1000 genomes]
rs3772041	0.86[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs3772042	0.86[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs3772043	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs3772044	0.95[CEU][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs3821341	0.81[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap]
rs4283455	0.82[EUR][1000 genomes]
rs4854243	0.83[EUR][1000 genomes]
rs4854244	0.81[EUR][1000 genomes]
rs4854247	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4854249	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6577012	0.86[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs6577013	0.86[CEU][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs6715813	0.86[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs6719098	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6723333	0.81[EUR][1000 genomes]
rs6725821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6741001	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs6750542	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs7574862	0.86[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs7580685	0.86[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs7585473	0.84[EUR][1000 genomes]
rs7585914	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7586229	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7594144	0.88[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs7602807	0.81[EUR][1000 genomes]
rs870393	0.81[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap]
rs872580	0.80[EUR][1000 genomes]
rs889851	0.86[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs889852	0.86[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs889853	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs918811	0.90[CEU][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs9678800	0.90[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs9989786	0.85[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1008945	chr2:95745367-96062107	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv817299	chr2:95799814-96159275	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1007627	chr2:95878031-95973743	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv535822	chr2:95878031-95973743	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv998370	chr2:95897299-96074071	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv535823	chr2:95897299-96074071	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv998014	chr2:95913278-96296630	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1966272	SRA1	trans	parietal	SCAN
rs1966272	KCNIP3	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95924000-95941200	Weak transcription	Right Ventricle	heart
2	chr2:95924400-95927000	Enhancers	Placenta Amnion	Placenta Amnion
3	chr2:95924400-95941400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:95924800-95926800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:95924800-95926800	Enhancers	Esophagus	oesophagus
6	chr2:95925000-95927200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:95925400-95926400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:95925400-95926800	Enhancers	Placenta	Placenta
9	chr2:95925400-95926800	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr2:95925400-95927600	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr2:95925400-95933200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:95925600-95926600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr2:95925600-95926800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:95925600-95926800	Strong transcription	Stomach Smooth Muscle	stomach
15	chr2:95925600-95953800	Weak transcription	Right Atrium	heart
16	chr2:95925800-95926800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:95925800-95934000	Weak transcription	Spleen	Spleen
18	chr2:95926000-95926200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:95926000-95926200	Flanking Active TSS	HMEC	breast
20	chr2:95926000-95926200	Flanking Active TSS	NHEK	skin
21	chr2:95926000-95927800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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