Variant report

Variant	rs7565772
Chromosome Location	chr2:95684417-95684418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:95682327..95685125-chr2:95786799..95789008,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144029	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10172167	0.86[CEU][hapmap]
rs17119148	0.95[CEU][hapmap];0.80[CHB][hapmap]
rs1875402	0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2291991	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2320619	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2320620	0.95[CEU][hapmap];0.89[CHB][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3105098	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3105099	0.90[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.85[MKK][hapmap];0.87[YRI][hapmap]
rs3105100	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3105101	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs3105104	0.95[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs3105105	0.90[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs3112225	0.95[CEU][hapmap];0.80[CHB][hapmap];0.85[YRI][hapmap]
rs3112228	0.95[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs3112229	0.80[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs3112230	0.89[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap]
rs3112982	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3112983	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs3112984	0.94[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3112985	0.89[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3112986	0.88[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3112987	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3112995	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs3112996	0.95[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs3112997	0.89[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap]
rs3113002	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.87[YRI][hapmap];0.80[ASN][1000 genomes]
rs4241315	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4555374	0.86[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs4564804	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs4854241	0.90[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4854243	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4854244	0.81[EUR][1000 genomes]
rs6708474	0.85[CEU][hapmap]
rs6723333	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7560571	0.91[CHB][hapmap]
rs7582368	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7585473	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs872580	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9324212	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000661	chr2:95327875-95739468	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1003666	chr2:95618109-95772924	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7565772	KCNIP3	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95664400-95690600	Weak transcription	Right Atrium	heart
2	chr2:95664800-95686200	Enhancers	Fetal Thymus	thymus
3	chr2:95674400-95686000	Weak transcription	Primary T cells from cord blood	blood
4	chr2:95676200-95685600	Weak transcription	Fetal Kidney	kidney
5	chr2:95681200-95685000	Weak transcription	Fetal Lung	lung
6	chr2:95681600-95684800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:95681600-95688200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:95682200-95685800	Enhancers	Esophagus	oesophagus
9	chr2:95682200-95690000	Enhancers	Brain Substantia Nigra	brain
10	chr2:95682600-95685600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:95683200-95685000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:95683400-95685000	Weak transcription	Brain Anterior Caudate	brain
13	chr2:95683400-95685200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr2:95683400-95685200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr2:95683400-95685400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:95683600-95685000	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:95683800-95685000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:95683800-95686800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:95684000-95684800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:95684000-95686400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:95684000-95687200	Enhancers	Placenta Amnion	Placenta Amnion
22	chr2:95684400-95684800	Weak transcription	Brain Angular Gyrus	brain
23	chr2:95684400-95685400	Enhancers	Thymus	Thymus

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