Variant report

Variant	rs17009341
Chromosome Location	chr4:85845116-85845117
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:85844433..85846847-chr4:85886096..85888500,2	MCF-7	breast:
2	chr4:85844299..85846003-chr4:85865441..85868769,3	MCF-7	breast:
3	chr4:85844090..85846010-chr4:85857826..85860121,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163625	Chromatin interaction
ENSG00000180769	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10029496	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10856851	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10856852	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11097026	1.00[CEU][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11097028	0.81[EUR][1000 genomes]
rs11730981	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11732309	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11732347	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12498637	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498787	0.86[EUR][1000 genomes]
rs12503215	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506456	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510410	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12511112	0.95[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap]
rs12640378	0.85[EUR][1000 genomes]
rs12648852	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13109918	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13114115	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13118671	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs13124246	0.87[EUR][1000 genomes]
rs13141322	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13148035	0.86[EUR][1000 genomes]
rs1484660	0.87[AMR][1000 genomes]
rs1508670	0.81[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs17009317	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs17009334	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs2046402	0.86[AMR][1000 genomes]
rs2046404	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2869216	0.95[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes]
rs28754901	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3098928	0.95[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap]
rs34239067	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34314581	0.87[EUR][1000 genomes]
rs4131745	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4376130	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4383611	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs4464556	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4470615	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4533765	0.90[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4590017	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs4624645	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4626191	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4634212	0.83[EUR][1000 genomes]
rs55871210	0.81[EUR][1000 genomes]
rs56194765	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6531777	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531782	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6531783	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs67045782	0.90[AMR][1000 genomes]
rs6815917	0.80[EUR][1000 genomes]
rs6833661	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835046	0.81[AMR][1000 genomes]
rs6847067	0.86[JPT][hapmap]
rs6847564	0.81[JPT][hapmap]
rs6847811	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857555	0.87[AMR][1000 genomes]
rs6858666	0.88[ASW][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.80[YRI][hapmap]
rs72664934	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72664952	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72664957	0.83[EUR][1000 genomes]
rs7654035	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7661609	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7663580	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7675324	0.86[EUR][1000 genomes]
rs7685537	0.86[JPT][hapmap];0.91[MEX][hapmap]
rs7692223	0.86[JPT][hapmap]
rs7694949	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7699226	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9684737	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9790649	0.85[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
rs17009341	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85781800-85848600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr4:85798800-85873200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:85809000-85872800	Weak transcription	A549	lung
4	chr4:85811800-85851200	Weak transcription	Esophagus	oesophagus
5	chr4:85813000-85858800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:85816000-85852400	Weak transcription	Left Ventricle	heart
7	chr4:85821600-85858400	Weak transcription	Pancreas	Pancrea
8	chr4:85825400-85848600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:85825400-85848600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:85825600-85848800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:85825600-85849000	Weak transcription	Fetal Intestine Large	intestine
12	chr4:85825600-85849000	Weak transcription	Fetal Muscle Leg	muscle
13	chr4:85826200-85845400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr4:85826400-85849200	Weak transcription	Fetal Stomach	stomach
15	chr4:85827200-85848800	Weak transcription	Ovary	ovary
16	chr4:85829200-85850000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:85829200-85866200	Weak transcription	Spleen	Spleen
18	chr4:85834600-85845600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:85835000-85848400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:85835200-85848400	Weak transcription	Fetal Lung	lung
21	chr4:85837600-85845600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr4:85837600-85858400	Weak transcription	Fetal Brain Female	brain
23	chr4:85837600-85859200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:85837800-85845600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:85837800-85849800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:85837800-85849800	Weak transcription	Fetal Kidney	kidney
27	chr4:85837800-85853200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr4:85837800-85858000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr4:85838200-85848400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr4:85838200-85848600	Weak transcription	Brain Germinal Matrix	brain
31	chr4:85838400-85853800	Weak transcription	Fetal Heart	heart
32	chr4:85838600-85848600	Weak transcription	Aorta	Aorta
33	chr4:85838600-85858600	Weak transcription	Liver	Liver
34	chr4:85838600-85858600	Weak transcription	Psoas Muscle	Psoas
35	chr4:85839200-85846600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr4:85839600-85858400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr4:85839800-85845400	Weak transcription	Brain Hippocampus Middle	brain
38	chr4:85839800-85845400	Weak transcription	Brain Substantia Nigra	brain
39	chr4:85839800-85848600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:85840000-85845800	Weak transcription	Fetal Brain Male	brain
41	chr4:85840200-85845400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr4:85840200-85848800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:85840400-85848800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:85842000-85848600	Weak transcription	Gastric	stomach
45	chr4:85842200-85845600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:85842200-85845600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr4:85842200-85848400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr4:85842200-85848600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:85842200-85848600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:85842200-85849200	Weak transcription	NHLF	lung

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