Variant report

Variant	rs2297003
Chromosome Location	chr9:13125201-13125202
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	JUND	chr9:13125167-13125809	SK-N-SH	brain:	n/a	chr9:13125449-13125459 chr9:13125449-13125459 chr9:13125449-13125459 chr9:13125446-13125457 chr9:13125448-13125459 chr9:13125450-13125459 chr9:13125449-13125459 chr9:13125448-13125460

Variant related genes	Relation type
MPDZ	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10116304	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10116749	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10122431	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10125770	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10511577	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10733254	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10738323	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10738324	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10738325	0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs10756454	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10756455	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10756456	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10756457	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10756458	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10756459	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10809906	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10809907	0.87[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10809908	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10809912	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10809920	0.81[JPT][hapmap]
rs10960955	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10960958	0.85[EUR][1000 genomes]
rs10960959	0.85[EUR][1000 genomes]
rs12351444	0.95[JPT][hapmap]
rs1330129	0.90[JPT][hapmap]
rs1331668	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1331670	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1331672	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1331673	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs1331674	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs1331675	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs1360058	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];0.99[ASN][1000 genomes]
rs1556421	0.91[CHD][hapmap];0.95[JPT][hapmap]
rs16930137	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1854414	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1854907	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1854908	0.96[CEU][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1854909	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1929541	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1999393	0.95[JPT][hapmap]
rs2225483	0.91[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2274856	0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs35068818	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3818595	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][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]
rs4237130	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58794982	0.84[ASN][1000 genomes]
rs6474753	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6474754	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6474755	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7024892	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7035244	0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7037618	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs7037704	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7039646	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7040347	0.88[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs7859465	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7867993	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7871112	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7871575	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9886797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[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];1.00[EUR][1000 genomes];1.00[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	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv917331	chr9:12941193-13146852	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv892578	chr9:12942956-13485035	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv892582	chr9:13085379-13147764	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13097800-13139400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:13101600-13141600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:13103200-13134600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:13103200-13137200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:13103200-13143400	Weak transcription	Pancreas	Pancrea
6	chr9:13103200-13163400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:13103200-13175600	Weak transcription	HepG2	liver
8	chr9:13103400-13134600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:13103800-13139400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:13104400-13137200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:13105600-13134800	Weak transcription	Lung	lung
12	chr9:13105600-13144600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:13106000-13153400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:13106600-13139200	Weak transcription	NHEK	skin
15	chr9:13109200-13138800	Weak transcription	Spleen	Spleen
16	chr9:13109200-13139400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:13111200-13134800	Weak transcription	Fetal Brain Male	brain
18	chr9:13111400-13128200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:13112200-13143600	Weak transcription	Gastric	stomach
20	chr9:13112400-13134600	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:13113400-13134800	Weak transcription	Psoas Muscle	Psoas
22	chr9:13114200-13135000	Weak transcription	NHLF	lung
23	chr9:13114400-13132200	Weak transcription	Brain Substantia Nigra	brain
24	chr9:13114600-13139200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:13114600-13139400	Weak transcription	NHDF-Ad	bronchial
26	chr9:13116000-13139800	Strong transcription	Liver	Liver
27	chr9:13117800-13125600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:13118000-13139000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:13118200-13126800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:13118200-13138800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:13118400-13125400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:13118400-13125600	Strong transcription	Adipose Nuclei	Adipose
33	chr9:13118400-13128400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:13118400-13139600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:13118800-13139600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr9:13118800-13139800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr9:13119000-13126600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:13119000-13137200	Weak transcription	Esophagus	oesophagus
39	chr9:13119400-13126000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr9:13119400-13126600	Strong transcription	HUVEC	blood vessel
41	chr9:13119600-13134600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr9:13119800-13125600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:13120400-13125400	Strong transcription	Osteobl	bone
44	chr9:13121200-13125400	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr9:13121200-13125600	Strong transcription	NH-A	brain
46	chr9:13121400-13125400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:13121400-13125600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr9:13121600-13125400	Strong transcription	Stomach Smooth Muscle	stomach
49	chr9:13121600-13225200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr9:13121800-13125600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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