Variant report

Variant	rs2922824
Chromosome Location	chr8:6313369-6313370
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	chr8:6313067..6315249-chr8:6315975..6317705,2	MCF-7	breast:

Extended variants
information (count: 146 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs1054073	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1054074	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11137029	0.87[ASN][1000 genomes]
rs1129703	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1129704	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1129706	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12545613	0.86[ASN][1000 genomes]
rs12545939	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12546890	0.97[ASN][1000 genomes]
rs12550299	0.86[ASN][1000 genomes]
rs12675930	0.87[ASN][1000 genomes]
rs12676907	0.87[ASN][1000 genomes]
rs12676922	0.87[ASN][1000 genomes]
rs12681195	0.85[ASN][1000 genomes]
rs13281967	0.82[ASN][1000 genomes]
rs13282022	0.82[ASN][1000 genomes]
rs13282577	0.82[ASN][1000 genomes]
rs1373306	0.94[EUR][1000 genomes]
rs1373307	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1530409	0.83[EUR][1000 genomes]
rs1550690	0.83[ASN][1000 genomes]
rs17077031	0.86[ASN][1000 genomes]
rs17077056	0.85[ASN][1000 genomes]
rs17077067	0.82[ASN][1000 genomes]
rs1867385	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1867386	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1868551	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1966818	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2034143	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2053618	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2083914	0.80[EUR][1000 genomes]
rs2166006	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2251956	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2254903	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2440395	0.87[ASN][1000 genomes]
rs2440403	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2440406	0.82[ASN][1000 genomes]
rs2440408	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2440411	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2440412	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2440413	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2440414	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2440415	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2440416	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2440419	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2440422	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2440423	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2440424	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2440427	0.80[AMR][1000 genomes]
rs2440432	0.82[ASN][1000 genomes]
rs2442485	0.82[ASN][1000 genomes]
rs2442497	0.86[ASN][1000 genomes]
rs2442499	0.88[EUR][1000 genomes]
rs2442500	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2442502	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2442503	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2442505	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2442506	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2442507	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2442510	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2442511	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2442512	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2442514	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2442515	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2442516	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2442518	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2442519	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2442520	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2442521	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2442522	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2442523	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2442524	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2442533	0.83[EUR][1000 genomes]
rs2515555	0.81[ASN][1000 genomes]
rs2515564	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2515568	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2515570	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2515571	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2515572	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2515573	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2515576	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2515592	0.82[ASN][1000 genomes]
rs2916723	0.81[ASN][1000 genomes]
rs2916739	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2916740	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2916741	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2916742	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2916743	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2916745	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2916746	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2916749	0.83[EUR][1000 genomes]
rs2916750	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2920658	0.84[AFR][1000 genomes]
rs2920659	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2920660	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2920661	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2920662	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2920665	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2920666	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920668	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2920669	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920671	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2920672	0.83[EUR][1000 genomes]
rs2920681	0.82[ASN][1000 genomes]
rs2922818	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2922819	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2922820	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2922821	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2922822	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2922823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2922833	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2979647	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2979648	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2979649	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2979650	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2979651	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2979652	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3020270	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3020275	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020278	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816402	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56073811	0.86[ASN][1000 genomes]
rs60915478	0.85[ASN][1000 genomes]
rs6559161	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6559162	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7001036	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7001056	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7002187	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7008037	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7008227	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73196802	0.82[ASN][1000 genomes]
rs7824209	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7833481	0.86[ASN][1000 genomes]
rs894895	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs930557	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs963754	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890034	chr8:5926632-6427868	Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv3506199	chr8:6116693-6536592	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	esv3506200	chr8:6116693-6536592	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv482828	chr8:6182711-6355710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv890055	chr8:6237397-6351252	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv933282	chr8:6261036-6440592	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1015981	chr8:6286575-6578450	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1027313	chr8:6286575-6920312	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2922824	CTD-2541M15.1	cis	Esophagus Muscularis	GTEx
rs2922824	MCPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6265000-6339200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr8:6282800-6313400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr8:6287600-6344400	Weak transcription	Small Intestine	intestine
4	chr8:6301000-6338400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr8:6302800-6313800	Weak transcription	Brain Angular Gyrus	brain
6	chr8:6302800-6339800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr8:6303000-6313400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr8:6303000-6313800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr8:6303000-6317200	Weak transcription	Brain Substantia Nigra	brain
10	chr8:6303000-6317800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr8:6303000-6319400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr8:6303000-6321000	Weak transcription	Psoas Muscle	Psoas
13	chr8:6303000-6321000	Weak transcription	Hela-S3	cervix
14	chr8:6303000-6322800	Weak transcription	Ovary	ovary
15	chr8:6303000-6322800	Weak transcription	Spleen	Spleen
16	chr8:6303000-6325000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr8:6303000-6325200	Weak transcription	Pancreas	Pancrea
18	chr8:6303000-6338200	Weak transcription	Gastric	stomach
19	chr8:6303000-6338200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr8:6303000-6338400	Weak transcription	Colonic Mucosa	Colon
21	chr8:6303000-6338400	Weak transcription	Right Ventricle	heart
22	chr8:6303000-6339400	Weak transcription	Placenta	Placenta
23	chr8:6303200-6316800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr8:6303200-6318200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr8:6303200-6318800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr8:6303200-6320400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr8:6303200-6321000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr8:6303200-6322600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr8:6303200-6322800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr8:6303200-6339400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr8:6303200-6339400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr8:6303200-6340000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr8:6303400-6313800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr8:6303400-6314600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr8:6303400-6320600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr8:6303400-6320800	Weak transcription	Colon Smooth Muscle	Colon
37	chr8:6303400-6321000	Weak transcription	Brain Anterior Caudate	brain
38	chr8:6303400-6321200	Weak transcription	HUVEC	blood vessel
39	chr8:6303600-6321600	Weak transcription	Brain Germinal Matrix	brain
40	chr8:6303800-6338400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr8:6304000-6313800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr8:6304000-6322600	Weak transcription	Fetal Brain Female	brain
43	chr8:6304000-6338000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr8:6304400-6318200	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr8:6304400-6360200	Weak transcription	Esophagus	oesophagus
46	chr8:6304600-6313400	Weak transcription	Fetal Intestine Small	intestine
47	chr8:6304600-6313800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr8:6304600-6317400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr8:6304600-6321200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr8:6304800-6314000	Weak transcription	Primary B cells from peripheral blood	blood

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