Variant report

Variant	rs2566885
Chromosome Location	chr7:128917587-128917588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:128911298..128913685-chr7:128916132..128918074,2	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1000676	0.86[JPT][hapmap]
rs10248810	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10257620	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10954226	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs10954230	0.86[JPT][hapmap]
rs11763056	0.93[ASN][1000 genomes]
rs11763325	0.98[ASN][1000 genomes]
rs11979476	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs12112374	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.98[ASN][1000 genomes]
rs12216567	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12534372	0.86[JPT][hapmap]
rs12540568	0.86[JPT][hapmap]
rs12667132	0.86[JPT][hapmap]
rs12668958	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs13226649	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1526900	0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1559486	0.80[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs17168512	0.97[ASN][1000 genomes]
rs1880854	0.93[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2056694	0.98[ASN][1000 genomes]
rs2103232	0.97[ASN][1000 genomes]
rs2402944	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2402945	0.97[ASN][1000 genomes]
rs2566876	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2566877	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2566886	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2694572	0.93[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2694574	0.89[CEU][hapmap];0.89[JPT][hapmap]
rs2718083	0.90[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2718084	0.81[ASW][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2718086	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2718089	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2718093	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2718096	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2718115	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4440569	0.98[ASN][1000 genomes]
rs4728163	0.86[JPT][hapmap]
rs4728164	0.86[JPT][hapmap]
rs4731569	0.82[ASN][1000 genomes]
rs4731572	0.86[JPT][hapmap]
rs4731575	0.85[JPT][hapmap]
rs56026912	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59659852	0.98[ASN][1000 genomes]
rs60275163	0.97[ASN][1000 genomes]
rs6467233	0.95[GIH][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs6467235	0.98[ASN][1000 genomes]
rs6467237	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6467240	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6467241	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6467242	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6467243	0.91[ASN][1000 genomes]
rs66538149	0.95[ASN][1000 genomes]
rs66864889	0.97[ASN][1000 genomes]
rs67520056	0.93[ASN][1000 genomes]
rs67997229	0.97[ASN][1000 genomes]
rs68076553	0.97[ASN][1000 genomes]
rs68184415	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68187585	0.91[ASN][1000 genomes]
rs6948252	0.93[ASN][1000 genomes]
rs6949950	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6966595	0.80[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.89[MKK][hapmap]
rs6967464	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6971917	0.93[ASN][1000 genomes]
rs6974155	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6980385	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.98[ASN][1000 genomes]
rs73472312	0.98[ASN][1000 genomes]
rs7778277	0.93[ASN][1000 genomes]
rs7782348	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7788327	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7792317	0.97[ASN][1000 genomes]
rs7794622	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7800983	0.80[ASN][1000 genomes]
rs7803052	0.97[ASN][1000 genomes]
rs7806089	0.95[ASN][1000 genomes]
rs822038	0.95[JPT][hapmap]
rs822040	0.80[CHD][hapmap];0.95[JPT][hapmap]
rs891545	0.93[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs963465	0.90[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9641846	0.93[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9641849	0.83[EUR][1000 genomes]
rs9649530	0.82[ASN][1000 genomes]
rs9649531	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349195	chr7:128887559-128918489	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv525482	chr7:128890812-129045191	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv516498	chr7:128901429-129072024	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2566885	KCP	cis	cerebellum	SCAN
rs2566885	LOC407835	cis	cerebellum	SCAN
rs2566885	SMO	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128897400-128919400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:128898800-128919600	Weak transcription	Right Ventricle	heart
3	chr7:128900000-128925000	Weak transcription	Psoas Muscle	Psoas
4	chr7:128902600-128934000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr7:128902800-128928600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr7:128903000-128929200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr7:128903200-128925000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:128903400-128931400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr7:128903400-128933800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:128905200-128922800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr7:128905800-128932200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:128907800-128924400	Weak transcription	Small Intestine	intestine
13	chr7:128909800-128925600	Weak transcription	Left Ventricle	heart
14	chr7:128910200-128924800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:128911000-128934400	Weak transcription	Brain Angular Gyrus	brain
16	chr7:128911800-128921400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr7:128911800-128925000	Weak transcription	Adipose Nuclei	Adipose
18	chr7:128911800-128930600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr7:128912000-128925000	Weak transcription	Brain Substantia Nigra	brain
20	chr7:128912000-128925000	Weak transcription	Ovary	ovary
21	chr7:128912000-128927000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr7:128912200-128925600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr7:128912200-128947000	Weak transcription	Pancreas	Pancrea
24	chr7:128913200-128940800	Weak transcription	Aorta	Aorta
25	chr7:128913400-128926000	Weak transcription	Fetal Thymus	thymus
26	chr7:128914000-128921600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr7:128914000-128934400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr7:128914200-128933400	Weak transcription	Primary B cells from cord blood	blood
29	chr7:128914400-128919200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr7:128914400-128919400	Weak transcription	HMEC	breast
31	chr7:128914400-128920800	Weak transcription	Dnd41	blood
32	chr7:128914400-128925000	Weak transcription	Brain Anterior Caudate	brain
33	chr7:128914600-128919200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr7:128914600-128919400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr7:128914600-128919600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr7:128914600-128922800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:128914600-128929000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr7:128914800-128918400	Weak transcription	Liver	Liver
39	chr7:128914800-128918600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr7:128914800-128919200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr7:128914800-128919200	Weak transcription	NHEK	skin
42	chr7:128914800-128919400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr7:128914800-128919400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr7:128914800-128919400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:128914800-128919400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr7:128914800-128922800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr7:128914800-128922800	Weak transcription	Esophagus	oesophagus
48	chr7:128914800-128923800	Weak transcription	Gastric	stomach
49	chr7:128914800-128924200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr7:128914800-128924800	Weak transcription	Fetal Stomach	stomach

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