Variant report

Variant	rs2920668
Chromosome Location	chr8:6314866-6314867
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	chr8:6313067..6315249-chr8:6315975..6317705,2	MCF-7	breast:

Extended variants
information (count: 130 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1054073	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1054074	0.91[EUR][1000 genomes]
rs11137029	0.84[ASN][1000 genomes]
rs1129703	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1129704	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1129706	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12545613	0.85[ASN][1000 genomes]
rs12545939	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12546890	0.93[ASN][1000 genomes]
rs12550299	0.85[ASN][1000 genomes]
rs12675930	0.84[ASN][1000 genomes]
rs12676907	0.84[ASN][1000 genomes]
rs12676922	0.84[ASN][1000 genomes]
rs12681195	0.82[ASN][1000 genomes]
rs1373306	0.91[EUR][1000 genomes]
rs1373307	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1530409	0.81[EUR][1000 genomes]
rs1550690	0.80[ASN][1000 genomes]
rs17077031	0.85[ASN][1000 genomes]
rs17077056	0.82[ASN][1000 genomes]
rs1867385	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1867386	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1868551	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1966818	0.80[EUR][1000 genomes]
rs2034143	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2053618	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2166006	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2251956	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2254903	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2440395	0.84[ASN][1000 genomes]
rs2440403	0.85[EUR][1000 genomes]
rs2440408	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2440411	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2440412	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2440413	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2440414	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2440415	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2440416	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2440419	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2440422	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2440423	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2440424	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2442497	0.85[ASN][1000 genomes]
rs2442499	0.85[EUR][1000 genomes]
rs2442500	0.82[EUR][1000 genomes]
rs2442502	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2442503	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2442505	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2442506	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2442507	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2442510	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2442511	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2442512	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2442514	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2442515	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2442516	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2442518	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2442519	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2442520	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2442521	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2442522	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2442523	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2442524	0.83[EUR][1000 genomes]
rs2442533	0.81[EUR][1000 genomes]
rs2515564	0.80[EUR][1000 genomes]
rs2515568	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2515570	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2515571	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2515572	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2515573	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2515576	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2916739	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2916740	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2916741	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2916742	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2916743	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2916745	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2916746	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2916749	0.81[EUR][1000 genomes]
rs2916750	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2920659	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920660	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2920661	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2920662	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2920665	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2920666	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2920669	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2920671	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920672	0.81[EUR][1000 genomes]
rs2922818	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2922819	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2922820	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2922821	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2922822	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2922823	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2922824	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2922833	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2979647	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2979648	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2979649	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2979650	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2979651	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2979652	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3020270	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3020275	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3020278	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3816402	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56073811	0.85[ASN][1000 genomes]
rs60915478	0.82[ASN][1000 genomes]
rs6559161	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6559162	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7001036	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7001056	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7002187	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7824209	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7833481	0.85[ASN][1000 genomes]
rs894895	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs930557	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs963754	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
11	nsv890056	chr8:6314486-6343727	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2920668	MCPH1	Cis_1M	lymphoblastoid	RTeQTL
rs2920668	CTD-2541M15.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:105 , 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	chr8:6287600-6344400	Weak transcription	Small Intestine	intestine
3	chr8:6301000-6338400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr8:6302800-6339800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr8:6303000-6317200	Weak transcription	Brain Substantia Nigra	brain
6	chr8:6303000-6317800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr8:6303000-6319400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr8:6303000-6321000	Weak transcription	Psoas Muscle	Psoas
9	chr8:6303000-6321000	Weak transcription	Hela-S3	cervix
10	chr8:6303000-6322800	Weak transcription	Ovary	ovary
11	chr8:6303000-6322800	Weak transcription	Spleen	Spleen
12	chr8:6303000-6325000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr8:6303000-6325200	Weak transcription	Pancreas	Pancrea
14	chr8:6303000-6338200	Weak transcription	Gastric	stomach
15	chr8:6303000-6338200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr8:6303000-6338400	Weak transcription	Colonic Mucosa	Colon
17	chr8:6303000-6338400	Weak transcription	Right Ventricle	heart
18	chr8:6303000-6339400	Weak transcription	Placenta	Placenta
19	chr8:6303200-6316800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr8:6303200-6318200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr8:6303200-6318800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr8:6303200-6320400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr8:6303200-6321000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr8:6303200-6322600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr8:6303200-6322800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr8:6303200-6339400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr8:6303200-6339400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr8:6303200-6340000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr8:6303400-6320600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr8:6303400-6320800	Weak transcription	Colon Smooth Muscle	Colon
31	chr8:6303400-6321000	Weak transcription	Brain Anterior Caudate	brain
32	chr8:6303400-6321200	Weak transcription	HUVEC	blood vessel
33	chr8:6303600-6321600	Weak transcription	Brain Germinal Matrix	brain
34	chr8:6303800-6338400	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr8:6304000-6322600	Weak transcription	Fetal Brain Female	brain
36	chr8:6304000-6338000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr8:6304400-6318200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr8:6304400-6360200	Weak transcription	Esophagus	oesophagus
39	chr8:6304600-6317400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr8:6304600-6321200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr8:6304800-6317200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr8:6304800-6323000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr8:6305000-6317000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr8:6305000-6317000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr8:6305200-6316800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr8:6305200-6320000	Weak transcription	Fetal Muscle Leg	muscle
47	chr8:6305800-6317200	Weak transcription	Brain Hippocampus Middle	brain
48	chr8:6305800-6319800	Weak transcription	Primary B cells from cord blood	blood
49	chr8:6305800-6322800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr8:6306000-6317000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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