Variant report

Variant	rs6559498
Chromosome Location	chr9:71989600-71989601
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10116389	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10746594	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10746613	0.89[AFR][1000 genomes]
rs10780334	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10780360	0.92[JPT][hapmap]
rs10780361	0.92[JPT][hapmap]
rs10867414	0.83[EUR][1000 genomes]
rs10867423	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10867481	0.84[AFR][1000 genomes]
rs12379338	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1334312	1.00[CEU][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1761290	0.85[AFR][1000 genomes]
rs1812971	0.87[AFR][1000 genomes]
rs1929896	0.87[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs2309431	1.00[ASW][hapmap];0.82[CEU][hapmap];0.92[GIH][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes]
rs2777866	0.82[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs2777878	0.82[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs2781521	0.82[CEU][hapmap];0.92[GIH][hapmap];0.84[LWK][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs2781522	0.82[CEU][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs2781527	0.88[AFR][1000 genomes]
rs35625426	0.85[AFR][1000 genomes]
rs3858105	1.00[CEU][hapmap]
rs3896424	0.82[AFR][1000 genomes]
rs3934600	0.82[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4237232	0.84[AFR][1000 genomes]
rs4237233	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4237234	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4483220	0.82[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs4484762	0.82[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs4503164	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4744886	0.94[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4744894	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62570234	0.82[AFR][1000 genomes]
rs6559488	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[GIH][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs6559489	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs6559512	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6559513	0.80[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6559527	0.80[AFR][1000 genomes]
rs7019551	0.86[CEU][hapmap]
rs7043451	1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs7044071	0.82[JPT][hapmap]
rs7046199	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7856778	0.82[CEU][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs7866250	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9314682	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6559498	TJP2	cis	cerebellum	SCAN
rs6559498	C9orf57	cis	cerebellum	SCAN
rs6559498	C18orf16	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71962200-71994200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:71963200-71991800	Weak transcription	Pancreas	Pancrea
3	chr9:71972600-71991800	Weak transcription	Right Atrium	heart
4	chr9:71972800-71991400	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:71977400-71992400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:71978800-71991600	Weak transcription	Left Ventricle	heart
7	chr9:71979000-72001800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:71983400-72001800	Weak transcription	Brain Anterior Caudate	brain
9	chr9:71985400-71994200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:71985400-72006600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr9:71985600-71989600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr9:71985600-71991000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:71985600-71991200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:71985600-71991400	Weak transcription	Colon Smooth Muscle	Colon
15	chr9:71985600-71992400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr9:71985800-71990200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:71986000-71990800	Weak transcription	HSMMtube	muscle
18	chr9:71986200-71990600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:71986600-71990000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:71986600-71991000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:71986600-71991000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:71986600-71991000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr9:71986600-71991200	Weak transcription	Stomach Mucosa	stomach
24	chr9:71986600-71991600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr9:71986600-71991800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:71986600-71991800	Weak transcription	Gastric	stomach
27	chr9:71986600-71992200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr9:71986600-72002600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr9:71986800-71989800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr9:71986800-71990000	Weak transcription	HMEC	breast
31	chr9:71986800-71990600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:71986800-71991000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr9:71986800-71991000	Weak transcription	Osteobl	bone
34	chr9:71986800-71991200	Weak transcription	NH-A	brain
35	chr9:71986800-71994200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr9:71987000-71991000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr9:71987000-71991000	Weak transcription	HUVEC	blood vessel
38	chr9:71987000-71991400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr9:71987000-71992200	Weak transcription	Brain Angular Gyrus	brain
40	chr9:71987600-71991800	Weak transcription	Psoas Muscle	Psoas
41	chr9:71988600-71989800	Enhancers	Fetal Heart	heart
42	chr9:71988800-71998600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr9:71989000-72002800	Weak transcription	Brain Substantia Nigra	brain
44	chr9:71989200-71989600	Enhancers	Right Ventricle	heart
45	chr9:71989200-71989800	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr9:71989200-71992200	Enhancers	Ovary	ovary
47	chr9:71989400-71990200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:71989600-71991600	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr9:71989600-71991800	Weak transcription	Right Ventricle	heart
50	chr9:71989600-71997000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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