Variant report

Variant	rs1546317
Chromosome Location	chr9:85640998-85640999
allele	A/C
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: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1008171	0.89[CEU][hapmap]
rs1010480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10115768	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10116216	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs10116254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10121156	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10121204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10121376	0.83[EUR][1000 genomes]
rs10121395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10126033	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10735559	0.89[CEU][hapmap]
rs10746694	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10780561	0.92[CEU][hapmap]
rs10780562	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10780563	1.00[CEU][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10780564	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10780565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10780567	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10867924	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10867925	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10867926	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10867927	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10867928	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10867929	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11139896	0.87[ASN][1000 genomes]
rs1125915	0.82[CEU][hapmap]
rs13302349	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1393562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393563	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1393564	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1393565	1.00[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1502682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1546315	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1546316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1580881	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];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2062761	0.81[CEU][hapmap]
rs2279814	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs29001503	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4146960	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4146961	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4301515	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4348583	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4355855	0.89[CEU][hapmap]
rs4385545	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4391505	0.89[CEU][hapmap]
rs4460464	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs4623517	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4628323	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4877244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4877725	0.89[CEU][hapmap]
rs6559694	1.00[CEU][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6559695	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7029133	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7045914	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7847666	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7853052	0.80[EUR][1000 genomes]
rs7854101	1.00[CEU][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7866666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867614	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs952450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs998119	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[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:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85603200-85643800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr9:85610800-85642000	Weak transcription	Fetal Intestine Large	intestine
3	chr9:85613600-85643400	Weak transcription	Colonic Mucosa	Colon
4	chr9:85617200-85645800	Weak transcription	Stomach Mucosa	stomach
5	chr9:85621000-85645400	Weak transcription	Gastric	stomach
6	chr9:85623600-85643200	Weak transcription	Fetal Intestine Small	intestine
7	chr9:85628600-85643400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr9:85630000-85641600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:85635600-85641400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr9:85635600-85641800	Weak transcription	Esophagus	oesophagus
11	chr9:85636200-85641400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:85636400-85643600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr9:85637400-85641400	Weak transcription	Pancreas	Pancrea
14	chr9:85637400-85643200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr9:85639200-85641200	Weak transcription	A549	lung
16	chr9:85639800-85645000	Enhancers	HMEC	breast
17	chr9:85640000-85641400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:85640000-85641600	Weak transcription	Osteobl	bone
19	chr9:85640000-85641800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:85640000-85641800	Weak transcription	NHLF	lung
21	chr9:85640200-85642000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr9:85640400-85641400	Weak transcription	NHDF-Ad	bronchial
23	chr9:85640400-85642000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:85640400-85644400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:85640400-85656400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr9:85640800-85641400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:85640800-85641800	Weak transcription	Placenta	Placenta

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