Variant report

Variant	rs884880
Chromosome Location	chr10:52163991-52163992
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52160595..52164108-chr10:52172645..52175372,3	MCF-7	breast:
2	chr10:52162771..52165523-chr10:52230742..52234155,3	MCF-7	breast:
3	chr10:52156579..52161749-chr10:52162901..52167145,5	K562	blood:
4	chr10:52161910..52166825-chr10:52176564..52180969,7	MCF-7	breast:
5	chr10:52163174..52165033-chr10:52169624..52171788,2	K562	blood:
6	chr10:52127520..52128296-chr10:52163800..52164644,2	MCF-7	breast:
7	chr10:52163746..52166986-chr10:52175766..52179128,4	MCF-7	breast:
8	chr10:52136009..52138905-chr10:52161513..52164062,2	K562	blood:
9	chr10:52163901..52167177-chr10:52381610..52384393,3	MCF-7	breast:
10	chr10:52154508..52157227-chr10:52160159..52164764,6	MCF-7	breast:
11	chr10:52158173..52160799-chr10:52163076..52165080,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225303	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10490963	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490964	1.00[ASW][hapmap];0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11005626	0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11005959	0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12257419	1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12262259	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1369860	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17438825	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17440448	0.88[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17518471	0.89[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17519121	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17519380	0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17721658	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721694	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721713	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17778152	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1916568	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1916569	0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1916571	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2060560	0.92[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2064759	0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs2117961	0.91[ASN][1000 genomes]
rs2117962	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255387	0.92[CHB][hapmap];0.84[JPT][hapmap];0.99[ASN][1000 genomes]
rs2255720	0.99[ASN][1000 genomes]
rs2255849	0.92[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2255853	0.92[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2255859	0.90[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs2574955	0.92[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2574956	0.92[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2574975	0.86[ASN][1000 genomes]
rs2574981	0.99[ASN][1000 genomes]
rs2688875	0.81[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs2688877	0.93[ASN][1000 genomes]
rs2688879	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2842102	0.99[ASN][1000 genomes]
rs2842105	0.99[ASN][1000 genomes]
rs2842106	0.99[ASN][1000 genomes]
rs2842107	0.92[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2842109	0.85[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs34672995	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34928652	0.92[ASN][1000 genomes]
rs3802537	0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4935152	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4935673	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4935703	0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4935713	0.87[ASN][1000 genomes]
rs4935729	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55773344	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55861418	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56078228	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56080689	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56133398	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56225400	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56268559	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56277433	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61559519	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61741330	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61856761	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61856763	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61856778	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61856782	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61856787	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61856788	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61856793	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61856794	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61856795	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61856828	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61856832	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61858062	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61858064	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61858065	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61858068	0.89[ASN][1000 genomes]
rs61858069	0.92[ASN][1000 genomes]
rs61858206	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61858207	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7067626	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7068430	1.00[ASW][hapmap];0.89[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs7069115	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082805	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7092753	0.92[ASN][1000 genomes]
rs72801752	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72801754	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72801768	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72801775	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72801776	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72801781	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7392702	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7475420	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7921632	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1053903	chr10:51886486-52163991	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1040661	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1051028	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1037118	chr10:51886486-52167442	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv948006	chr10:52127164-52177684	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs884880	MSMB	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52142600-52170200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr10:52147000-52176600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:52148600-52165800	Weak transcription	Primary B cells from cord blood	blood
4	chr10:52152400-52167600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr10:52155400-52165800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr10:52155800-52165800	Weak transcription	Primary T cells from cord blood	blood
7	chr10:52156200-52164200	Weak transcription	Brain Anterior Caudate	brain
8	chr10:52156200-52165800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr10:52156200-52170200	Weak transcription	Pancreas	Pancrea
10	chr10:52156600-52165800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr10:52157000-52170800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr10:52157200-52164000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:52157200-52170000	Weak transcription	Gastric	stomach
14	chr10:52157200-52177600	Weak transcription	Spleen	Spleen
15	chr10:52157400-52164000	Weak transcription	Left Ventricle	heart
16	chr10:52157400-52165400	Weak transcription	HMEC	breast
17	chr10:52157400-52167200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr10:52157400-52167200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr10:52157400-52170000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr10:52157600-52165400	Weak transcription	NHEK	skin
21	chr10:52157800-52164000	Weak transcription	Placenta	Placenta
22	chr10:52157800-52164200	Weak transcription	Psoas Muscle	Psoas
23	chr10:52157800-52166000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr10:52157800-52167400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr10:52157800-52168800	Weak transcription	NHDF-Ad	bronchial
26	chr10:52157800-52169200	Weak transcription	HSMM	muscle
27	chr10:52157800-52172000	Weak transcription	Fetal Lung	lung
28	chr10:52157800-52173200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr10:52157800-52175400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:52157800-52176800	Weak transcription	Lung	lung
31	chr10:52158400-52164200	Weak transcription	Adipose Nuclei	Adipose
32	chr10:52158400-52166000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr10:52158800-52169400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr10:52158800-52172200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr10:52159000-52166000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr10:52160400-52164600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr10:52160800-52176800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr10:52161200-52164000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr10:52161200-52166000	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr10:52161600-52165000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr10:52161800-52164000	Enhancers	Hela-S3	cervix
42	chr10:52162000-52166000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr10:52162600-52164800	Enhancers	HepG2	liver
44	chr10:52163000-52164600	Genic enhancers	K562	blood
45	chr10:52163200-52164000	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr10:52163200-52164400	Enhancers	Brain Angular Gyrus	brain
47	chr10:52163200-52170200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr10:52163400-52164000	Enhancers	A549	lung
49	chr10:52163400-52164400	Enhancers	Brain Substantia Nigra	brain
50	chr10:52163400-52164400	Enhancers	Fetal Kidney	kidney

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