Variant report

Variant	rs3098928
Chromosome Location	chr4:85679803-85679804
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10007879	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11097024	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12511112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13118671	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs13145705	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1385263	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1484661	0.91[JPT][hapmap]
rs1508670	0.81[JPT][hapmap]
rs17009247	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17009249	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17009317	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs17009334	0.90[JPT][hapmap]
rs17009341	0.95[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap]
rs2046402	0.82[EUR][1000 genomes]
rs2046404	0.86[JPT][hapmap]
rs2170935	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2218323	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2869216	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36036245	0.82[EUR][1000 genomes]
rs3747680	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs4529041	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6531775	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6531777	0.95[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap]
rs67045782	0.82[EUR][1000 genomes]
rs6825852	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs6829807	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs6835046	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6838727	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs6839516	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6847067	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6847564	0.95[JPT][hapmap]
rs6853486	0.91[CEU][hapmap];0.91[MEX][hapmap]
rs6858666	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72664926	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7654035	0.87[JPT][hapmap]
rs7668460	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7685537	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7699226	0.95[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv532738	chr4:85590841-85777997	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3098928	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85619200-85726000	Weak transcription	Hela-S3	cervix
2	chr4:85636400-85701200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:85657000-85704200	Weak transcription	Psoas Muscle	Psoas
4	chr4:85664000-85703400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:85664000-85703600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:85664200-85703600	Weak transcription	Right Ventricle	heart
7	chr4:85668600-85703800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:85668800-85680000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:85669600-85703600	Weak transcription	Aorta	Aorta
10	chr4:85670600-85700600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:85672200-85702400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:85672400-85700600	Weak transcription	Spleen	Spleen
13	chr4:85672400-85707000	Weak transcription	Colonic Mucosa	Colon
14	chr4:85672800-85700600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:85672800-85703600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:85672800-85703600	Weak transcription	Esophagus	oesophagus
17	chr4:85672800-85703600	Weak transcription	NHLF	lung
18	chr4:85673000-85695600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:85673000-85700600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:85673200-85685000	Weak transcription	NH-A	brain
21	chr4:85673200-85689600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr4:85673200-85692400	Weak transcription	Brain Hippocampus Middle	brain
23	chr4:85673200-85703600	Weak transcription	HepG2	liver
24	chr4:85673600-85700800	Weak transcription	Lung	lung
25	chr4:85673800-85700600	Weak transcription	Pancreas	Pancrea
26	chr4:85674600-85702200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr4:85675000-85695400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr4:85675000-85700600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:85675200-85702800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:85675200-85703600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr4:85675400-85681400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:85675400-85685000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:85675400-85692200	Weak transcription	Ovary	ovary
34	chr4:85675600-85703600	Weak transcription	Fetal Brain Male	brain
35	chr4:85675800-85700400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr4:85676200-85700800	Weak transcription	HMEC	breast
37	chr4:85676400-85692200	Weak transcription	Brain Germinal Matrix	brain
38	chr4:85676400-85695600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:85676400-85698200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr4:85676600-85685600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:85676600-85685600	Weak transcription	Adipose Nuclei	Adipose
42	chr4:85676600-85686800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr4:85676600-85688800	Weak transcription	Fetal Intestine Large	intestine
44	chr4:85676600-85689000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr4:85676600-85689000	Weak transcription	Fetal Lung	lung
46	chr4:85676600-85689000	Weak transcription	Left Ventricle	heart
47	chr4:85676600-85691400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:85676600-85692200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr4:85676600-85694600	Weak transcription	NHDF-Ad	bronchial
50	chr4:85676600-85695200	Weak transcription	Colon Smooth Muscle	Colon

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