Variant report

Variant	rs16949418
Chromosome Location	chr17:45991240-45991241
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45990771..45994045-chr17:45997430..46001241,5	MCF-7	breast:
2	chr17:45985387..45988064-chr17:45989640..45992704,3	MCF-7	breast:
3	chr17:45990204..45992323-chr17:45993152..45994828,2	MCF-7	breast:
4	chr17:45897631..45900192-chr17:45989508..45992239,2	K562	blood:
5	chr17:45989573..45991691-chr17:45999240..46001944,2	K562	blood:
6	chr17:45974701..45976946-chr17:45989221..45991463,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006025	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11079800	0.82[ASW][hapmap];0.92[CEU][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11079802	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11650395	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11651753	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs11653445	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12939572	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12942207	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16949720	0.90[JPT][hapmap]
rs2002136	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs2256020	0.82[YRI][hapmap]
rs2325748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525095	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs2525109	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2525110	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2597169	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2875735	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs3764394	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3764398	0.86[ASN][1000 genomes]
rs4794331	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs59811700	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71377324	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7207225	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7220104	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs72833480	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72833491	0.98[ASN][1000 genomes]
rs72840233	1.00[ASN][1000 genomes]
rs8066574	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8079333	0.82[EUR][1000 genomes]
rs8182261	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9899097	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16949418	CALCOCO2	cis	parietal	SCAN
rs16949418	SP2	cis	lymphoblastoid	seeQTL
rs16949418	VAT1	cis	cerebellum	SCAN
rs16949418	PNPO	cis	Nerve Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45974600-45992000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr17:45975000-45993400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:45975200-45999400	Weak transcription	Fetal Kidney	kidney
4	chr17:45975200-46000400	Weak transcription	Small Intestine	intestine
5	chr17:45975600-45992800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr17:45975800-46000600	Weak transcription	Hela-S3	cervix
7	chr17:45976400-45993200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr17:45976400-45995400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:45977600-45992800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:45977600-45995000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr17:45977800-45992000	Weak transcription	Dnd41	blood
12	chr17:45977800-45992600	Weak transcription	Fetal Intestine Large	intestine
13	chr17:45977800-45992600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr17:45977800-45992800	Weak transcription	GM12878-XiMat	blood
15	chr17:45979800-46000400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr17:45980000-45992600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:45980000-45992800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr17:45980000-45992800	Weak transcription	Brain Germinal Matrix	brain
19	chr17:45980200-46001800	Weak transcription	K562	blood
20	chr17:45980200-46002400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr17:45980200-46006400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr17:45980400-45992400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr17:45980400-45993600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr17:45980800-45992600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr17:45982400-46000600	Weak transcription	Stomach Mucosa	stomach
26	chr17:45982600-45992600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr17:45982600-45992600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr17:45982600-45992800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr17:45982600-45996200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr17:45982800-45993000	Weak transcription	NHEK	skin
31	chr17:45983000-45993800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr17:45983000-46001000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr17:45983000-46004000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr17:45983200-45992400	Weak transcription	Colonic Mucosa	Colon
35	chr17:45983200-45992600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr17:45983200-45992600	Weak transcription	Gastric	stomach
37	chr17:45983200-45993200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:45983200-45995200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr17:45983200-45995200	Weak transcription	HUVEC	blood vessel
40	chr17:45983200-46000400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr17:45983200-46001200	Weak transcription	A549	lung
42	chr17:45983200-46018200	Weak transcription	Fetal Brain Male	brain
43	chr17:45983400-45992800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr17:45983400-46000600	Weak transcription	NHDF-Ad	bronchial
45	chr17:45983600-45992600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr17:45983600-45992800	Weak transcription	Esophagus	oesophagus
47	chr17:45983800-45992600	Weak transcription	Primary B cells from cord blood	blood
48	chr17:45984000-45992600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr17:45984000-45993600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr17:45984200-45992000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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