Variant report

Variant	rs9828178
Chromosome Location	chr3:142171303-142171304
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	chr3:142164997..142168564-chr3:142170242..142173896,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114127	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10935465	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1129393	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11925693	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12695761	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13061823	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13065075	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13067795	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13075471	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13085998	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13093869	0.81[EUR][1000 genomes]
rs13098343	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2227928	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2227930	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2862743	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2862744	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28708455	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3922730	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4273389	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4441672	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4597728	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57177110	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6440082	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6440086	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6440087	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6440088	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6440089	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6440090	0.82[EUR][1000 genomes]
rs6440091	0.80[EUR][1000 genomes]
rs6440092	0.82[EUR][1000 genomes]
rs6440093	0.82[EUR][1000 genomes]
rs6440094	0.82[EUR][1000 genomes]
rs6768093	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6769786	0.82[AMR][1000 genomes]
rs6770155	0.82[EUR][1000 genomes]
rs6772400	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6775583	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6775718	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6777255	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6780250	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782400	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6785675	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6791816	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6792259	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6799752	0.82[EUR][1000 genomes]
rs7610557	0.82[EUR][1000 genomes]
rs7623524	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7627694	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7630130	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7634158	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7641330	0.81[ASN][1000 genomes]
rs7647573	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7651071	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7652687	0.83[EUR][1000 genomes]
rs9683085	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9808914	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9808943	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9816736	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820770	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825207	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9826786	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9846960	0.81[ASN][1000 genomes]
rs9847364	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9855140	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9855919	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9869842	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9871402	0.86[EUR][1000 genomes]
rs9876254	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9879995	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv523945	chr3:141933649-142219542	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1000083	chr3:141956718-142172666	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	nsv528954	chr3:142164017-142219542	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142167200-142174800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:142167200-142174800	Weak transcription	Lung	lung
3	chr3:142167200-142176800	Weak transcription	Gastric	stomach
4	chr3:142167200-142178800	Weak transcription	Small Intestine	intestine
5	chr3:142167200-142187600	Weak transcription	Esophagus	oesophagus
6	chr3:142167200-142192400	Weak transcription	Pancreas	Pancrea
7	chr3:142167400-142175600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:142167400-142176400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:142167400-142176800	Weak transcription	Placenta	Placenta
10	chr3:142167400-142179600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:142167400-142199400	Weak transcription	Colonic Mucosa	Colon
12	chr3:142167400-142199600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:142167400-142234600	Weak transcription	Psoas Muscle	Psoas
14	chr3:142167600-142171600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:142167600-142171600	Weak transcription	K562	blood
16	chr3:142167600-142176400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:142167600-142177000	Weak transcription	Right Ventricle	heart
18	chr3:142167600-142177000	Weak transcription	NH-A	brain
19	chr3:142167600-142177400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:142167600-142177600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:142167600-142177600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:142167600-142180000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:142167600-142180000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:142167600-142187200	Weak transcription	Fetal Brain Male	brain
25	chr3:142167600-142191800	Weak transcription	Fetal Brain Female	brain
26	chr3:142167600-142199600	Weak transcription	Ovary	ovary
27	chr3:142167600-142200000	Weak transcription	HSMMtube	muscle
28	chr3:142167600-142203000	Weak transcription	Brain Angular Gyrus	brain
29	chr3:142167800-142171400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:142167800-142171600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:142167800-142171800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:142167800-142175800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:142167800-142176000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:142167800-142176200	Weak transcription	HUVEC	blood vessel
35	chr3:142167800-142177000	Weak transcription	Brain Anterior Caudate	brain
36	chr3:142167800-142177000	Weak transcription	NHDF-Ad	bronchial
37	chr3:142167800-142177400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:142167800-142177600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:142167800-142177600	Weak transcription	NHEK	skin
40	chr3:142167800-142179000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr3:142167800-142179800	Weak transcription	Brain Substantia Nigra	brain
42	chr3:142167800-142180000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr3:142167800-142180200	Weak transcription	HepG2	liver
44	chr3:142167800-142184800	Weak transcription	Colon Smooth Muscle	Colon
45	chr3:142167800-142186400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr3:142167800-142188800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr3:142167800-142190400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr3:142167800-142199400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:142167800-142200000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr3:142167800-142200000	Weak transcription	Muscle Satellite Cultured Cells	--

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