Variant report

Variant	rs2690042
Chromosome Location	chr6:25288271-25288272
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr6:25288204-25288378	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25277697..25280622-chr6:25286931..25288666,2	MCF-7	breast:
2	chr6:25282721..25284707-chr6:25287856..25289519,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207286	TF binding region
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs12055697	0.80[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs16890366	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1883393	0.95[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs2143023	0.86[ASN][1000 genomes]
rs2690111	0.83[CHB][hapmap]
rs2744287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712904	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4712905	0.95[CHB][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4712906	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4712907	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55967593	0.86[ASN][1000 genomes]
rs55999195	0.86[ASN][1000 genomes]
rs58191968	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60084615	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6456664	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6456665	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6456666	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6456668	0.85[ASN][1000 genomes]
rs6903148	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6906812	0.85[ASN][1000 genomes]
rs6913606	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6913886	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6914439	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6914514	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6914654	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6914798	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6914930	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6915270	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6917631	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6921343	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6923529	0.96[ASN][1000 genomes]
rs6927238	0.82[ASN][1000 genomes]
rs6938281	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6938594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs730711	0.93[ASN][1000 genomes]
rs73392399	0.96[ASN][1000 genomes]
rs73396126	0.84[ASN][1000 genomes]
rs7741580	0.84[ASN][1000 genomes]
rs7743750	0.93[ASN][1000 genomes]
rs7746942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7746969	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7755701	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7756143	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7758529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7759796	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs7759879	0.84[ASN][1000 genomes]
rs7760067	0.86[ASN][1000 genomes]
rs7760151	0.86[ASN][1000 genomes]
rs7764111	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs9295654	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]
rs9348671	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9356974	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9356975	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs9366616	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379752	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379753	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9379754	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs9393639	0.86[ASN][1000 genomes]
rs9461132	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9461134	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9461135	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9461136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9467466	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]
rs999039	1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv883484	chr6:25237288-25303100	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2690042	NKAPL	cis	parietal	SCAN
rs2690042	LRRC16A	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25280800-25302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:25281200-25290400	Weak transcription	Ovary	ovary
3	chr6:25281200-25290600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:25281200-25293600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:25281200-25296000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:25281400-25288400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:25281400-25290600	Weak transcription	Adipose Nuclei	Adipose
8	chr6:25281400-25292000	Weak transcription	Fetal Lung	lung
9	chr6:25281400-25295800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:25281400-25295800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:25281400-25295800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:25281400-25296000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:25281600-25290400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:25281600-25290600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:25281600-25290600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:25281600-25293800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:25281600-25293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:25281600-25294400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr6:25281600-25295600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:25281600-25295800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:25281600-25295800	Weak transcription	Thymus	Thymus
22	chr6:25281600-25296000	Weak transcription	Primary T cells from cord blood	blood
23	chr6:25281600-25296000	Weak transcription	Fetal Thymus	thymus
24	chr6:25281600-25296400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr6:25281800-25288400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr6:25281800-25288400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr6:25281800-25290600	Weak transcription	Fetal Intestine Large	intestine
28	chr6:25281800-25291600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:25281800-25292400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr6:25281800-25295800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:25282000-25292400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:25282200-25293800	Weak transcription	Lung	lung
33	chr6:25282800-25296400	Weak transcription	Hela-S3	cervix
34	chr6:25283600-25290400	Weak transcription	Left Ventricle	heart
35	chr6:25284600-25290600	Weak transcription	A549	lung
36	chr6:25285800-25290600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr6:25286400-25289000	Enhancers	HMEC	breast
38	chr6:25286400-25295000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:25286600-25288600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:25286800-25300800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr6:25287400-25288600	Enhancers	Duodenum Mucosa	Duodenum
42	chr6:25287600-25288400	Enhancers	Aorta	Aorta
43	chr6:25287600-25290600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr6:25287800-25288400	Enhancers	Small Intestine	intestine
45	chr6:25287800-25288400	Genic enhancers	NHEK	skin
46	chr6:25287800-25289000	Enhancers	Right Atrium	heart
47	chr6:25287800-25296000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:25288000-25288400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:25288000-25289000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:25288000-25289400	Enhancers	HUES48 Cell Line	embryonic stem cell

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