Variant report

Variant	rs9684737
Chromosome Location	chr4:85851965-85851966
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10029496	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10856851	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10856852	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs11097026	1.00[CEU][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11097028	0.82[EUR][1000 genomes]
rs11730981	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11732309	0.87[EUR][1000 genomes]
rs11732347	0.87[EUR][1000 genomes]
rs12498637	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498787	0.87[EUR][1000 genomes]
rs12503215	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506456	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510410	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12511112	0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap]
rs12640378	0.86[EUR][1000 genomes]
rs12648852	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13109918	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13114115	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13118671	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs13124246	0.88[EUR][1000 genomes]
rs13141322	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13148035	0.87[EUR][1000 genomes]
rs1484660	0.86[AMR][1000 genomes]
rs1508670	0.81[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs17009317	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs17009334	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs17009341	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046402	0.85[AMR][1000 genomes]
rs2046404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2869216	0.82[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes]
rs28754901	0.91[EUR][1000 genomes]
rs3098928	0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap]
rs34239067	0.86[EUR][1000 genomes]
rs34314581	0.88[EUR][1000 genomes]
rs4131745	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4376130	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4383611	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs4464556	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4470615	0.85[EUR][1000 genomes]
rs4533765	0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs4590017	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs4624645	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4626191	0.87[EUR][1000 genomes]
rs4634212	0.84[EUR][1000 genomes]
rs55871210	0.82[EUR][1000 genomes]
rs56194765	0.87[EUR][1000 genomes]
rs58074983	0.81[EUR][1000 genomes]
rs6531777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531782	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs6531783	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs67045782	0.89[AMR][1000 genomes]
rs67624868	0.81[EUR][1000 genomes]
rs6815917	0.81[EUR][1000 genomes]
rs6820517	0.80[EUR][1000 genomes]
rs6833661	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847067	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6847564	0.81[JPT][hapmap]
rs6847811	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857555	0.86[AMR][1000 genomes]
rs6858666	0.88[ASW][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap]
rs72664934	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs72664952	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72664957	0.82[EUR][1000 genomes]
rs7654035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7661609	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7663580	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs7675324	0.87[EUR][1000 genomes]
rs7685537	0.86[JPT][hapmap];0.95[MEX][hapmap]
rs7692223	0.86[JPT][hapmap]
rs7694949	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7699226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9790649	0.86[EUR][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	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv427684	chr4:85668487-85863446	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv508295	chr4:85822802-85885027	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9684737	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85798800-85873200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:85809000-85872800	Weak transcription	A549	lung
3	chr4:85813000-85858800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr4:85816000-85852400	Weak transcription	Left Ventricle	heart
5	chr4:85821600-85858400	Weak transcription	Pancreas	Pancrea
6	chr4:85829200-85866200	Weak transcription	Spleen	Spleen
7	chr4:85837600-85858400	Weak transcription	Fetal Brain Female	brain
8	chr4:85837600-85859200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:85837800-85853200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr4:85837800-85858000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:85838400-85853800	Weak transcription	Fetal Heart	heart
12	chr4:85838600-85858600	Weak transcription	Liver	Liver
13	chr4:85838600-85858600	Weak transcription	Psoas Muscle	Psoas
14	chr4:85839600-85858400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr4:85842200-85852400	Weak transcription	Adipose Nuclei	Adipose
16	chr4:85842200-85857800	Weak transcription	Colon Smooth Muscle	Colon
17	chr4:85842400-85858400	Weak transcription	HMEC	breast
18	chr4:85842800-85858000	Weak transcription	HUVEC	blood vessel
19	chr4:85844400-85854400	Weak transcription	HepG2	liver
20	chr4:85844600-85854000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:85845600-85882800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:85846000-85852400	Weak transcription	NHEK	skin
23	chr4:85846400-85852400	Weak transcription	Brain Angular Gyrus	brain
24	chr4:85846400-85858400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:85846600-85852600	Weak transcription	Brain Hippocampus Middle	brain
26	chr4:85846600-85858200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr4:85846800-85852400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:85846800-85852600	Weak transcription	Brain Anterior Caudate	brain
29	chr4:85847000-85860200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr4:85848200-85853000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:85848400-85852600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr4:85848400-85852800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:85848400-85852800	Strong transcription	HSMM	muscle
34	chr4:85848400-85853000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:85848400-85853400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:85848400-85853400	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr4:85848400-85853400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:85848400-85853400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr4:85848400-85853600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr4:85848400-85853600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:85848400-85857800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr4:85848600-85852400	Weak transcription	Brain Substantia Nigra	brain
43	chr4:85848600-85852800	Strong transcription	Brain Germinal Matrix	brain
44	chr4:85848600-85853400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:85848600-85853600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:85848800-85852000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:85848800-85853000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr4:85848800-85853400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:85848800-85853400	Strong transcription	Fetal Lung	lung
50	chr4:85848800-85858400	Weak transcription	Small Intestine	intestine

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