Variant report

Variant	rs2947260
Chromosome Location	chr8:19125413-19125414
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:19123737..19126710-chr8:19170516..19173345,2	MCF-7	breast:
2	chr8:19125143..19125678-chr8:19171239..19172025,2	MCF-7	breast:
3	chr8:18769464..18770410-chr8:19124856..19125711,4	K562	blood:

Variant related genes	Relation type
ENSG00000104611	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10088667	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10091480	0.84[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10091481	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10092550	0.88[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10105631	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10108694	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204027	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11779774	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1193287	0.89[JPT][hapmap]
rs1193288	0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs1193290	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1193291	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1193292	0.88[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1193293	0.96[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1193294	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1193297	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1193305	0.84[ASN][1000 genomes]
rs1193308	0.84[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs1193309	0.84[ASN][1000 genomes]
rs13261970	0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1473939	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1473940	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1514702	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1514704	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1915404	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1915406	0.82[ASN][1000 genomes]
rs1915407	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1915408	0.80[ASN][1000 genomes]
rs1967513	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2139762	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2139763	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2176925	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2244965	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2244976	0.82[EUR][1000 genomes]
rs2672225	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2672226	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2672260	0.82[EUR][1000 genomes]
rs2672262	0.83[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2672264	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2683279	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2683280	0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2683285	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2683314	0.82[CEU][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs2683319	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2943422	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2943426	0.86[ASN][1000 genomes]
rs2943427	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2943430	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2947261	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2947262	0.86[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2947263	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34123475	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34192188	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34254629	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34265536	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34267592	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35604334	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35651150	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4922006	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4922007	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55811677	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55846624	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6586822	0.82[ASN][1000 genomes]
rs6586823	0.84[ASN][1000 genomes]
rs7814080	0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7841513	0.84[ASN][1000 genomes]
rs871668	0.81[CHB][hapmap]
rs991589	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026466	chr8:18433493-19271274	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv539520	chr8:18433493-19271274	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1015395	chr8:18489538-19370258	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv429907	chr8:18578720-19398220	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv917232	chr8:18585309-19208665	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv890610	chr8:18749120-19260599	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv949745	chr8:18826830-19363963	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv1016482	chr8:18834807-19339487	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv890614	chr8:18838764-19274793	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv533109	chr8:18845845-19456780	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv1016993	chr8:18855623-19311731	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	nsv890615	chr8:18989735-19181921	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv890616	chr8:18989735-19197809	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv1033229	chr8:19081684-19271274	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
16	nsv1033297	chr8:19108472-19150023	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv1034119	chr8:19115084-19164833	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	nsv465599	chr8:19115136-19159082	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	nsv610747	chr8:19115136-19159082	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
20	nsv465600	chr8:19116030-19156100	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv610748	chr8:19116030-19156100	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	nsv610749	chr8:19116030-19160915	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2947260	ATP6V1B2	cis	cerebellum	SCAN
rs2947260	NAT2	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19121600-19129400	Weak transcription	Spleen	Spleen
2	chr8:19122400-19129800	Weak transcription	Pancreas	Pancrea
3	chr8:19123200-19129800	Weak transcription	Gastric	stomach
4	chr8:19124000-19125800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr8:19124400-19125800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr8:19124600-19125600	Enhancers	Muscle Satellite Cultured Cells	--
7	chr8:19124600-19125600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr8:19124600-19125600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr8:19124600-19125600	Enhancers	Brain Hippocampus Middle	brain
10	chr8:19124600-19125600	Enhancers	HMEC	breast
11	chr8:19124600-19125600	Enhancers	NHDF-Ad	bronchial
12	chr8:19124600-19125600	Enhancers	NHLF	lung
13	chr8:19124600-19125800	Enhancers	Fetal Lung	lung
14	chr8:19124600-19126000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr8:19124600-19126000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr8:19124800-19125600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr8:19124800-19125600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr8:19124800-19125600	Enhancers	Fetal Heart	heart
19	chr8:19124800-19125600	Enhancers	Fetal Stomach	stomach
20	chr8:19124800-19125600	Flanking Active TSS	Hela-S3	cervix
21	chr8:19124800-19125600	Enhancers	NHEK	skin
22	chr8:19124800-19125800	Enhancers	Adipose Nuclei	Adipose
23	chr8:19125000-19125600	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr8:19125000-19125600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr8:19125000-19125600	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr8:19125000-19125600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr8:19125000-19125600	Enhancers	Primary B cells from peripheral blood	blood
28	chr8:19125000-19125600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
29	chr8:19125000-19125600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
30	chr8:19125000-19125600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
31	chr8:19125000-19125600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr8:19125000-19125600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr8:19125000-19125600	Enhancers	Colon Smooth Muscle	Colon
34	chr8:19125000-19125600	Enhancers	Fetal Brain Male	brain
35	chr8:19125000-19125600	Enhancers	Fetal Intestine Small	intestine
36	chr8:19125000-19125600	Enhancers	Fetal Muscle Leg	muscle
37	chr8:19125000-19125600	Enhancers	Right Atrium	heart
38	chr8:19125000-19125600	Enhancers	HSMM	muscle
39	chr8:19125000-19125800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr8:19125000-19125800	Enhancers	Fetal Intestine Large	intestine
41	chr8:19125000-19126000	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr8:19125000-19126000	Enhancers	Stomach Mucosa	stomach
43	chr8:19125200-19125600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr8:19125200-19125600	Enhancers	Brain Cingulate Gyrus	brain
45	chr8:19125200-19125600	Enhancers	Right Ventricle	heart
46	chr8:19125200-19125600	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr8:19125200-19126400	Enhancers	Liver	Liver
48	chr8:19125400-19125600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr8:19125400-19125600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr8:19125400-19125600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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