Variant report

Variant	rs1580881
Chromosome Location	chr9:85642312-85642313
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:85639962..85642383-chr9:85676276..85678231,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf103-7	chr9:85634340-85642318	predAs_engstrom06_AI205792_1

Variant related genes	Relation type
ENSG00000165105	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1008171	0.89[CEU][hapmap]
rs1010480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10115768	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10116216	0.81[CEU][hapmap]
rs10116254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10121156	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10121204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10121376	0.81[EUR][1000 genomes]
rs10121395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10126033	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10735559	0.89[CEU][hapmap]
rs10746694	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10780561	0.92[CEU][hapmap]
rs10780562	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10780563	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10780564	0.85[AMR][1000 genomes]
rs10780565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10780567	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10867924	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10867925	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10867926	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10867927	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10867928	1.00[CEU][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10867929	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10867930	0.80[AMR][1000 genomes]
rs11139896	0.86[ASN][1000 genomes]
rs1125915	0.82[CEU][hapmap]
rs13302349	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1393562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1393563	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1393564	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1393565	1.00[CEU][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes]
rs1502682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1502683	0.89[CEU][hapmap]
rs1502684	0.89[CEU][hapmap]
rs1502685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1546315	1.00[CEU][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1546316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1546317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1976455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2062761	0.81[CEU][hapmap];0.80[AMR][1000 genomes]
rs2279814	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs29001503	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4146960	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4146961	1.00[CEU][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4301515	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4348583	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4355855	0.89[CEU][hapmap]
rs4385545	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4391505	0.89[CEU][hapmap]
rs4460464	0.81[CEU][hapmap]
rs4623517	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4628323	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4877244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4877725	0.89[CEU][hapmap]
rs6559694	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6559695	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7019227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7024864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7029133	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7043325	0.81[EUR][1000 genomes]
rs7045914	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7847666	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7854101	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7866666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7867614	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs952450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs998119	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050771	chr9:85416931-85643417	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv893511	chr9:85495968-85833127	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85603200-85643800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr9:85613600-85643400	Weak transcription	Colonic Mucosa	Colon
3	chr9:85617200-85645800	Weak transcription	Stomach Mucosa	stomach
4	chr9:85621000-85645400	Weak transcription	Gastric	stomach
5	chr9:85623600-85643200	Weak transcription	Fetal Intestine Small	intestine
6	chr9:85628600-85643400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:85636400-85643600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr9:85637400-85643200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr9:85639800-85645000	Enhancers	HMEC	breast
10	chr9:85640400-85644400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:85640400-85656400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr9:85641200-85643200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:85641400-85642800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:85641400-85643000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:85641400-85643400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr9:85641400-85643400	Enhancers	HSMM	muscle
17	chr9:85641400-85643400	Enhancers	NHDF-Ad	bronchial
18	chr9:85641400-85644800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:85641400-85645000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:85641400-85645000	Enhancers	NHEK	skin
21	chr9:85641600-85643200	Enhancers	Osteobl	bone
22	chr9:85641600-85644400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:85641800-85642400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:85641800-85642400	Enhancers	Esophagus	oesophagus
25	chr9:85641800-85642400	Flanking Active TSS	A549	lung
26	chr9:85641800-85643000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:85641800-85643000	Enhancers	Placenta	Placenta
28	chr9:85641800-85643000	Enhancers	NHLF	lung
29	chr9:85641800-85643200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:85641800-85643400	Enhancers	Hela-S3	cervix
31	chr9:85642000-85642400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr9:85642000-85642400	Enhancers	Fetal Intestine Large	intestine
33	chr9:85642000-85642400	Enhancers	Placenta Amnion	Placenta Amnion
34	chr9:85642000-85642600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:85642000-85643200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:85642000-85643200	Flanking Active TSS	NH-A	brain
37	chr9:85642000-85643800	Weak transcription	Pancreas	Pancrea
38	chr9:85642200-85642800	Enhancers	HSMMtube	muscle

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