Variant report

Variant	rs13308560
Chromosome Location	chr7:97948323-97948324
allele	C/T
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	POLR2A	chr7:97948300-97948863	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:97946793..97949697-chr7:97951339..97953964,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272950	TF binding region
ENSG00000272950	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10226454	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10228934	0.82[EUR][1000 genomes]
rs10267597	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10277669	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10280254	0.93[EUR][1000 genomes]
rs12704987	0.86[AFR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13307956	1.00[EUR][1000 genomes]
rs1468339	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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1631779	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635611	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1635613	0.92[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[EUR][1000 genomes]
rs1635614	0.92[ASW][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap]
rs1688601	0.92[ASW][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap]
rs1688604	0.92[ASW][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap]
rs1966359	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1985594	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2906183	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34294017	0.97[EUR][1000 genomes]
rs35636211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35658212	0.96[EUR][1000 genomes]
rs4075058	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4448203	0.96[EUR][1000 genomes]
rs73391087	0.91[EUR][1000 genomes]
rs757669	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs757670	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7783403	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7791314	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv888760	chr7:97816327-97965016	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv831067	chr7:97860169-98065528	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv1026477	chr7:97869446-98034129	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv1016826	chr7:97926133-97963717	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97914200-97958400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:97919200-97957600	Weak transcription	Right Atrium	heart
3	chr7:97923400-97952000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr7:97924600-97952200	Weak transcription	Fetal Kidney	kidney
5	chr7:97924600-97952800	Weak transcription	NH-A	brain
6	chr7:97933000-97948400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr7:97933600-97952000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:97935800-97951800	Weak transcription	Right Ventricle	heart
9	chr7:97935800-97968600	Weak transcription	Hela-S3	cervix
10	chr7:97937600-97952200	Weak transcription	NHLF	lung
11	chr7:97937800-97950600	Weak transcription	Spleen	Spleen
12	chr7:97937800-97951800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr7:97938200-97951000	Weak transcription	Left Ventricle	heart
14	chr7:97939000-97948800	Strong transcription	A549	lung
15	chr7:97939200-97948600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr7:97939200-97948600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr7:97939200-97951800	Weak transcription	Osteobl	bone
18	chr7:97942000-97950200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr7:97942600-97950600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr7:97943000-97952200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:97943200-97949400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:97943600-97949400	Strong transcription	Liver	Liver
23	chr7:97943800-97948600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr7:97944200-97949400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr7:97944200-97951800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr7:97944600-97952000	Weak transcription	NHDF-Ad	bronchial
27	chr7:97944800-97983400	Weak transcription	HepG2	liver
28	chr7:97945000-97951800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr7:97945200-97951600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:97945200-97951600	Weak transcription	Adipose Nuclei	Adipose
31	chr7:97945200-97968400	Weak transcription	HMEC	breast
32	chr7:97945800-97950200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:97946000-97950200	Strong transcription	Fetal Intestine Small	intestine
34	chr7:97946000-97951800	Weak transcription	Fetal Intestine Large	intestine
35	chr7:97946000-97952200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:97946000-97952200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr7:97946400-97952000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr7:97946600-97948600	Strong transcription	Fetal Stomach	stomach
39	chr7:97946800-97948800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr7:97947000-97948400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr7:97947000-97948800	Strong transcription	Esophagus	oesophagus
42	chr7:97947000-97950000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr7:97947000-97951600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr7:97947000-97952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:97947200-97949200	Strong transcription	Gastric	stomach
46	chr7:97947200-97950200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr7:97947400-97948400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:97947400-97949000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr7:97947400-97950800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr7:97947400-97950800	Weak transcription	Stomach Mucosa	stomach

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