Variant report

Variant	rs9896922
Chromosome Location	chr17:64513860-64513861
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:64513488..64516427-chr17:64525867..64528816,2	MCF-7	breast:
2	chr17:64509877..64512323-chr17:64512992..64515530,3	MCF-7	breast:
3	chr17:64513672..64517176-chr17:64520746..64523284,3	K562	blood:
4	chr17:64503626..64507528-chr17:64509993..64514174,5	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1473933	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473934	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1514653	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17771145	0.90[LWK][hapmap]
rs1877846	1.00[ASN][1000 genomes]
rs1877847	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877848	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.98[ASN][1000 genomes]
rs1980118	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2056071	0.88[CEU][hapmap];0.88[JPT][hapmap]
rs228870	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs228874	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs228877	1.00[ASN][1000 genomes]
rs228878	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs228879	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs228881	0.86[EUR][1000 genomes]
rs228884	0.88[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs228887	0.83[EUR][1000 genomes]
rs228888	0.83[EUR][1000 genomes]
rs2361484	1.00[ASN][1000 genomes]
rs2361485	1.00[ASN][1000 genomes]
rs2535659	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2885290	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs4270211	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4375700	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4622543	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs4791053	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4791054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4791055	0.98[ASN][1000 genomes]
rs4791060	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs6504439	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6504440	0.94[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7211424	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7218008	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7218053	1.00[ASN][1000 genomes]
rs7218480	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7221053	0.87[ASN][1000 genomes]
rs7225362	0.94[ASN][1000 genomes]
rs8064886	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068988	0.96[ASN][1000 genomes]
rs8068989	0.98[ASN][1000 genomes]
rs8069282	0.92[ASN][1000 genomes]
rs8070470	1.00[ASN][1000 genomes]
rs8079527	0.86[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs9896483	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9896956	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897124	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9897534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9898205	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9913336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9915432	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057876	chr17:64401469-64802341	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv543407	chr17:64401469-64802341	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv457887	chr17:64410915-64518507	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv575898	chr17:64410915-64518507	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv817351	chr17:64420296-64742555	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv948353	chr17:64454960-64619767	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv948335	chr17:64454960-64745690	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1056765	chr17:64486268-64661890	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1058004	chr17:64504644-64592577	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1058272	chr17:64507560-64592577	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1066300	chr17:64510410-64591463	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9896922	EFCAB3	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:64490400-64520800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:64491000-64517800	Weak transcription	Dnd41	blood
3	chr17:64504200-64540600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr17:64505200-64527200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:64505600-64518600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:64505800-64517000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr17:64505800-64519200	Weak transcription	Right Ventricle	heart
8	chr17:64505800-64527800	Weak transcription	Pancreas	Pancrea
9	chr17:64506000-64519200	Weak transcription	Small Intestine	intestine
10	chr17:64506200-64520600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr17:64506400-64518000	Weak transcription	Ovary	ovary
12	chr17:64506400-64527800	Weak transcription	K562	blood
13	chr17:64506600-64514000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr17:64506600-64517000	Weak transcription	NHLF	lung
15	chr17:64506600-64517600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr17:64506600-64518200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr17:64506600-64519000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr17:64506600-64519200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr17:64506800-64514000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr17:64507200-64522200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr17:64507600-64514800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr17:64507800-64519000	Weak transcription	HSMM	muscle
23	chr17:64507800-64519000	Weak transcription	HSMMtube	muscle
24	chr17:64508200-64518000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:64510600-64518800	Weak transcription	NHEK	skin
26	chr17:64510600-64521400	Enhancers	Brain Anterior Caudate	brain
27	chr17:64510800-64519200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr17:64511000-64517400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr17:64511000-64518200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr17:64511000-64518600	Weak transcription	Osteobl	bone
31	chr17:64511000-64518800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr17:64511600-64520000	Weak transcription	Primary T cells from cord blood	blood
33	chr17:64511800-64516200	Enhancers	Brain Substantia Nigra	brain
34	chr17:64511800-64518600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr17:64512000-64518000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr17:64512000-64518200	Weak transcription	Stomach Mucosa	stomach
37	chr17:64512400-64514200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr17:64512400-64518200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr17:64512400-64520600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr17:64513000-64514000	Enhancers	Psoas Muscle	Psoas
41	chr17:64513200-64515600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr17:64513200-64519600	Weak transcription	Fetal Intestine Small	intestine
43	chr17:64513200-64521200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr17:64513400-64514000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr17:64513400-64514000	Enhancers	Liver	Liver
46	chr17:64513400-64514200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr17:64513400-64514400	Enhancers	A549	lung
48	chr17:64513400-64514600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr17:64513400-64515400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr17:64513400-64515600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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