Variant report

Variant	rs9467466
Chromosome Location	chr6:25312915-25312916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25298383..25300116-chr6:25311036..25313925,3	MCF-7	breast:
2	chr6:25307442..25309429-chr6:25310773..25313440,2	K562	blood:
3	chr6:25278102..25281759-chr6:25312379..25314512,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs12055697	0.87[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16890366	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1883393	0.98[CHD][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs2143023	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2690042	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2690111	0.83[CHB][hapmap]
rs2744287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4712904	0.93[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4712905	0.95[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4712906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712907	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55967593	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs55999195	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58191968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60084615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6456664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456666	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456668	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6903148	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906812	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6913606	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913886	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914439	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6914514	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914654	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6914798	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914930	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915270	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6917631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6921343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923529	0.96[ASN][1000 genomes]
rs6927238	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6938281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs730711	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs73392399	0.96[ASN][1000 genomes]
rs73396126	0.90[ASN][1000 genomes]
rs7741580	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7743750	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7746942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746969	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755701	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756143	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7758529	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759796	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7759828	0.81[ASN][1000 genomes]
rs7759879	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7760067	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7760151	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7764111	0.90[CHB][hapmap];0.83[JPT][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9295654	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295655	0.94[LWK][hapmap]
rs9348671	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9356974	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9356975	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs9366616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366617	0.81[ASW][hapmap];0.93[LWK][hapmap];0.82[AFR][1000 genomes]
rs9379752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9379754	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap]
rs9393639	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9461132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461134	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999039	0.93[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv16338	chr6:25312436-25315638	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9467466	NKAPL	cis	parietal	SCAN
rs9467466	LRRC16A	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25290400-25313400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:25301400-25313400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:25303200-25314800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:25303400-25315400	Weak transcription	Fetal Kidney	kidney
5	chr6:25305000-25324400	Weak transcription	Left Ventricle	heart
6	chr6:25306600-25331400	Weak transcription	Spleen	Spleen
7	chr6:25309200-25313400	Weak transcription	Ovary	ovary
8	chr6:25310200-25313000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:25310200-25313600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:25310200-25313800	Enhancers	Fetal Intestine Large	intestine
11	chr6:25310200-25314200	Enhancers	Fetal Intestine Small	intestine
12	chr6:25310200-25316800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:25310400-25313800	Enhancers	Duodenum Mucosa	Duodenum
14	chr6:25310400-25319400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr6:25310800-25315000	Weak transcription	Brain Anterior Caudate	brain
16	chr6:25311200-25314000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:25311400-25313800	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr6:25311400-25313800	Enhancers	Stomach Mucosa	stomach
19	chr6:25311400-25313800	Enhancers	HSMM	muscle
20	chr6:25311400-25314400	Enhancers	Osteobl	bone
21	chr6:25311600-25313000	Flanking Active TSS	Hela-S3	cervix
22	chr6:25311600-25313200	Enhancers	HSMMtube	muscle
23	chr6:25311600-25313200	Enhancers	NHLF	lung
24	chr6:25311600-25313400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr6:25311600-25313800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr6:25311600-25313800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr6:25311600-25313800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:25311600-25313800	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr6:25311600-25313800	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr6:25311600-25313800	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr6:25311600-25313800	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr6:25311600-25313800	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr6:25311600-25314000	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr6:25311600-25314200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr6:25311600-25314200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:25311600-25314400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr6:25311600-25315400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:25311600-25317200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:25311600-25317200	Enhancers	Fetal Lung	lung
40	chr6:25311800-25313200	Enhancers	Primary hematopoietic stem cells	blood
41	chr6:25311800-25313400	Enhancers	Primary T cells from cord blood	blood
42	chr6:25311800-25313800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr6:25311800-25313800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:25311800-25313800	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr6:25311800-25314000	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr6:25312000-25313000	Weak transcription	Aorta	Aorta
47	chr6:25312000-25313400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr6:25312000-25313400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:25312000-25313400	Weak transcription	Lung	lung
50	chr6:25312000-25313600	Weak transcription	Placenta	Placenta

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