Variant report

Variant	rs816671
Chromosome Location	chr9:98575014-98575015
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98572020..98575622-chr9:98635383..98638974,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTCH1-3	chr9:98568370-98576204	NONHSAT133392

Variant related genes	Relation type
ENSG00000182150	Chromatin interaction
ENSG00000175611	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10121403	0.86[ASN][1000 genomes]
rs10481647	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs10739632	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs10739787	0.84[AMR][1000 genomes]
rs10760675	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs10818017	0.84[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs10983622	0.93[ASN][1000 genomes]
rs10983692	0.92[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs10983739	0.92[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs10983773	0.92[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs10983818	0.92[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs12004422	1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs12375861	0.92[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs12553442	0.85[ASN][1000 genomes]
rs1410783	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1928253	0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs2117432	0.92[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs2164156	0.92[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs2164157	0.92[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs2770837	0.98[ASN][1000 genomes]
rs583716	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs585223	0.81[ASN][1000 genomes]
rs591579	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs601916	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs615866	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs631273	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs643815	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs6479036	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs667018	0.82[AMR][1000 genomes]
rs680754	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs683829	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs689627	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs689749	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs689871	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs689979	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs690222	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs690304	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs690335	0.85[ASN][1000 genomes]
rs690563	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs700963	0.92[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs7865593	0.82[AMR][1000 genomes]
rs7874897	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs816676	0.92[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs816681	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9409321	0.92[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs9409322	0.92[CHB][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]

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	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98548400-98578400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:98557400-98577200	Weak transcription	Pancreas	Pancrea
3	chr9:98569800-98575800	Weak transcription	Aorta	Aorta
4	chr9:98569800-98576200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr9:98570000-98575400	Weak transcription	Fetal Kidney	kidney
6	chr9:98570400-98575800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:98570400-98577400	Weak transcription	Brain Anterior Caudate	brain
8	chr9:98570400-98577600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:98570400-98577600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr9:98570400-98577600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr9:98570400-98580800	Weak transcription	Fetal Intestine Small	intestine
12	chr9:98570400-98585800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr9:98570400-98589200	Weak transcription	Left Ventricle	heart
14	chr9:98570400-98589200	Weak transcription	Right Ventricle	heart
15	chr9:98570400-98593200	Weak transcription	Gastric	stomach
16	chr9:98570400-98593800	Weak transcription	Right Atrium	heart
17	chr9:98570600-98576000	Weak transcription	NHLF	lung
18	chr9:98570600-98579200	Weak transcription	Liver	Liver
19	chr9:98570600-98579600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:98570600-98585000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr9:98570800-98576600	Weak transcription	HUVEC	blood vessel
22	chr9:98570800-98601400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr9:98571000-98575200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:98571000-98582000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:98571200-98577200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr9:98571400-98575800	Weak transcription	Ovary	ovary
27	chr9:98572400-98579000	Weak transcription	Primary T cells from cord blood	blood
28	chr9:98572800-98582400	Weak transcription	Brain Germinal Matrix	brain
29	chr9:98573000-98585400	Weak transcription	Thymus	Thymus
30	chr9:98573200-98575600	Weak transcription	Fetal Intestine Large	intestine
31	chr9:98573600-98576200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr9:98573800-98577200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:98574000-98576200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr9:98574000-98576400	Weak transcription	Brain Angular Gyrus	brain
35	chr9:98574200-98575800	Strong transcription	Fetal Lung	lung
36	chr9:98574200-98576000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:98574200-98576000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:98574200-98576200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:98574200-98576400	Weak transcription	Brain Substantia Nigra	brain
40	chr9:98574600-98577600	Weak transcription	Fetal Stomach	stomach

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