Variant report

Variant	rs17009317
Chromosome Location	chr4:85769856-85769857
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:85768280..85770094-chr4:85885997..85888803,2	MCF-7	breast:
2	chr4:85764070..85765619-chr4:85768603..85770984,2	K562	blood:
3	chr4:85763786..85765619-chr4:85768603..85770984,3	K562	blood:

Variant related genes	Relation type
ENSG00000163625	Chromatin interaction
ENSG00000180769	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10856852	0.84[TSI][hapmap]
rs11097026	0.81[CEU][hapmap]
rs11097028	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12500519	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12501525	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12502409	0.85[EUR][1000 genomes]
rs12502559	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12503330	0.82[EUR][1000 genomes]
rs12511112	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs13118671	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13125323	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13139541	0.83[EUR][1000 genomes]
rs13141072	0.82[EUR][1000 genomes]
rs1484661	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1508670	1.00[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17009334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17009341	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs2046404	0.81[CEU][hapmap]
rs2218323	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs2869216	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs3098928	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs35190829	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35892581	0.82[EUR][1000 genomes]
rs3747680	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs4383611	0.86[ASW][hapmap];0.85[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs4533765	0.84[TSI][hapmap]
rs4590017	0.86[ASW][hapmap];0.90[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs55871210	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56094216	0.84[EUR][1000 genomes]
rs58074983	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6531777	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs6531782	0.84[TSI][hapmap]
rs6531783	0.80[ASW][hapmap];0.90[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs66965560	0.80[EUR][1000 genomes]
rs67624868	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6815917	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6816534	0.80[EUR][1000 genomes]
rs6820517	0.86[EUR][1000 genomes]
rs6825852	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs6829807	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6838727	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs6847067	0.90[JPT][hapmap]
rs6847564	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6858666	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs72664928	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72664957	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7654035	0.81[CEU][hapmap]
rs7661609	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs7663580	0.84[TSI][hapmap]
rs7682896	0.81[EUR][1000 genomes]
rs7685537	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs7690054	0.82[EUR][1000 genomes]
rs7692223	0.90[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs7694949	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs7695054	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7699226	0.81[CEU][hapmap];0.88[TSI][hapmap]

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	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17009317	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85697400-85772800	Weak transcription	Small Intestine	intestine
2	chr4:85701600-85783000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:85705400-85770000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:85708600-85777400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:85709000-85781600	Weak transcription	Esophagus	oesophagus
6	chr4:85709200-85770200	Weak transcription	Psoas Muscle	Psoas
7	chr4:85722200-85787600	Weak transcription	Gastric	stomach
8	chr4:85723000-85821000	Weak transcription	Pancreas	Pancrea
9	chr4:85723200-85770400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr4:85723200-85777000	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:85724000-85781400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:85724000-85786600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:85727800-85783200	Weak transcription	Colonic Mucosa	Colon
14	chr4:85731400-85791600	Weak transcription	Lung	lung
15	chr4:85735800-85777000	Weak transcription	Aorta	Aorta
16	chr4:85736400-85790600	Weak transcription	NHEK	skin
17	chr4:85739400-85777000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:85742600-85783200	Weak transcription	Fetal Brain Male	brain
19	chr4:85742800-85777000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:85751600-85783000	Weak transcription	Stomach Mucosa	stomach
21	chr4:85751800-85770000	Weak transcription	HMEC	breast
22	chr4:85753200-85783400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:85760200-85777000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr4:85760800-85783400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:85761400-85780200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:85762000-85770200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:85762000-85774000	Weak transcription	Fetal Intestine Small	intestine
28	chr4:85762000-85781400	Weak transcription	Fetal Stomach	stomach
29	chr4:85762200-85777200	Weak transcription	Osteobl	bone
30	chr4:85762800-85777000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr4:85763600-85772000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr4:85765200-85770200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:85765400-85771600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:85765400-85771800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr4:85766000-85771200	Strong transcription	HUVEC	blood vessel
36	chr4:85766400-85777000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr4:85767600-85770400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:85767600-85771400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr4:85767600-85772000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:85767800-85771000	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:85767800-85771400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:85767800-85771400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr4:85768000-85771200	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr4:85768000-85771200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr4:85768000-85771200	Strong transcription	Fetal Intestine Large	intestine
46	chr4:85768000-85771200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr4:85768000-85771600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:85768000-85772200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:85768200-85777000	Weak transcription	Right Atrium	heart
50	chr4:85768600-85770000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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