Variant report

Variant	rs9392354
Chromosome Location	chr6:2028237-2028238
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1609057..1611446-chr6:2026298..2028309,2	MCF-7	breast:
2	chr6:1607895..1612984-chr6:2025307..2029705,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054598	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11242730	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11242734	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11242735	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12055694	0.87[CHD][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12164011	0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12530335	0.95[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12661847	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17134651	0.86[CHD][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4580917	0.82[CHD][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55635233	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56098578	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60898782	0.83[AMR][1000 genomes]
rs62390706	0.87[EUR][1000 genomes]
rs62390709	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62390733	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62392573	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs671240	0.82[CHB][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6920883	0.95[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6921994	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6923662	0.85[ASN][1000 genomes]
rs6924265	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6935616	0.95[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6935760	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7745086	0.95[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7749136	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7753375	0.95[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7759455	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7768100	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9378319	0.88[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9378666	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9378667	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9378668	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9378670	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9378671	0.95[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9378672	0.95[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9378676	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9378684	0.82[AMR][1000 genomes]
rs9391941	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9391943	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9391944	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9392348	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs9392352	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9392353	1.00[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9392356	0.81[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9392358	0.88[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9392371	0.86[JPT][hapmap]
rs9405539	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9405540	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9405541	0.90[CHD][hapmap];0.88[MEX][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9405542	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9405546	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
4	nsv1032727	chr6:1900622-2064690	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv538095	chr6:1900622-2064690	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv883386	chr6:1910108-2122454	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv981098	chr6:2008599-2102267	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv527735	chr6:2028237-2097654	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9392354	WRNIP1	cis	parietal	SCAN
rs9392354	BPHL	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2006200-2034800	Weak transcription	HepG2	liver
2	chr6:2019800-2040000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:2021600-2028600	Weak transcription	GM12878-XiMat	blood
4	chr6:2022200-2030600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr6:2022200-2031600	Weak transcription	Esophagus	oesophagus
6	chr6:2022400-2035000	Weak transcription	Gastric	stomach
7	chr6:2022400-2042800	Weak transcription	Right Atrium	heart
8	chr6:2022400-2055600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:2022400-2080600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:2022600-2028800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:2022600-2028800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:2022600-2028800	Weak transcription	Stomach Mucosa	stomach
13	chr6:2023800-2028800	Weak transcription	Fetal Thymus	thymus
14	chr6:2024000-2028600	Weak transcription	Thymus	Thymus
15	chr6:2024000-2028800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:2024600-2028400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:2024600-2028600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr6:2024800-2028600	Weak transcription	Primary T cells from cord blood	blood
19	chr6:2024800-2028600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr6:2024800-2028600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr6:2024800-2028600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr6:2025000-2028600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr6:2025000-2028600	Weak transcription	Dnd41	blood
24	chr6:2026600-2028600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:2026600-2030200	Weak transcription	Pancreas	Pancrea
26	chr6:2026600-2031600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:2026800-2031000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr6:2027000-2029000	Weak transcription	Small Intestine	intestine
29	chr6:2027000-2035000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:2027200-2029800	Weak transcription	Brain Germinal Matrix	brain
31	chr6:2027400-2030600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:2028000-2028600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:2028200-2028800	Enhancers	HUVEC	blood vessel

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