Variant report

Variant	rs3011794
Chromosome Location	chr10:52316590-52316591
allele	C/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52313061..52318898-chr10:52381919..52385253,10	MCF-7	breast:
2	chr10:52315809..52317364-chr10:52382275..52385092,2	K562	blood:
3	chr10:52315239..52317200-chr10:52324724..52326608,3	K562	blood:
4	chr10:52313546..52319488-chr10:52380502..52386285,13	K562	blood:
5	chr10:52310270..52314455-chr10:52315610..52319835,4	MCF-7	breast:
6	chr10:52316576..52318310-chr10:52369103..52371692,2	K562	blood:
7	chr10:52315813..52318278-chr10:52376288..52379260,2	K562	blood:
8	chr10:52310656..52316983-chr10:52334408..52339466,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction
ENSG00000226200	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10508931	1.00[ASW][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.86[AFR][1000 genomes]
rs10826273	1.00[MKK][hapmap]
rs11006166	0.91[ASN][1000 genomes]
rs11006179	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11006183	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11006185	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11006190	1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11006191	1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11006193	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs11006194	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11006197	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11006200	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs11006213	1.00[ASW][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.86[AFR][1000 genomes]
rs11006219	0.82[ASN][1000 genomes]
rs11006229	0.85[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs11006233	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs11006237	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11006238	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11006358	0.83[MKK][hapmap]
rs11006433	1.00[MKK][hapmap]
rs11006477	1.00[MKK][hapmap]
rs1203375	0.82[MEX][hapmap]
rs1203382	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs1203386	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs1203390	0.83[ASN][1000 genomes]
rs1203393	0.86[ASN][1000 genomes]
rs1203394	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs1203395	0.83[ASN][1000 genomes]
rs1203401	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1203403	0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1203405	0.83[ASN][1000 genomes]
rs1203407	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs1203409	0.95[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1203410	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs1203411	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1203418	0.84[JPT][hapmap];1.00[MEX][hapmap];0.80[ASN][1000 genomes]
rs1203420	0.80[ASN][1000 genomes]
rs1203421	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs12358348	1.00[MKK][hapmap]
rs1740761	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17496403	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs17496500	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs17581567	1.00[MKK][hapmap]
rs17582633	1.00[MKK][hapmap]
rs1810576	0.86[ASN][1000 genomes]
rs1916567	0.84[JPT][hapmap]
rs2221	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2574985	0.84[JPT][hapmap];1.00[MEX][hapmap]
rs2983347	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2983350	0.94[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2983354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2983357	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983368	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2983369	0.88[ASN][1000 genomes]
rs2983370	0.81[AMR][1000 genomes]
rs2983371	0.88[ASN][1000 genomes]
rs3011770	0.85[CEU][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes]
rs3011771	0.88[ASN][1000 genomes]
rs3011773	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3011779	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011780	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011782	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3011783	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3011786	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3011787	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3011788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011789	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011790	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011793	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3011801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7072826	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs7921226	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs920136	0.84[JPT][hapmap];1.00[MEX][hapmap]
rs956794	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3011794	MSMB	cis	parietal	SCAN
rs3011794	PARG	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52280200-52328000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:52299600-52320600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:52300800-52322800	Weak transcription	Primary B cells from cord blood	blood
4	chr10:52301600-52327200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr10:52305400-52329600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr10:52306000-52319000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr10:52306000-52321400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr10:52306000-52322000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr10:52306000-52331800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr10:52308000-52337200	Weak transcription	Primary T cells from cord blood	blood
11	chr10:52310400-52323800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr10:52310600-52323600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr10:52310600-52327200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:52311000-52323600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr10:52311000-52335800	Weak transcription	Esophagus	oesophagus
16	chr10:52311600-52316800	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr10:52312000-52316600	Enhancers	Brain Angular Gyrus	brain
18	chr10:52312000-52317000	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr10:52312600-52321000	Weak transcription	NH-A	brain
20	chr10:52312800-52319800	Enhancers	NHLF	lung
21	chr10:52312800-52335800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr10:52312800-52335800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr10:52313000-52316600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr10:52313000-52316800	Enhancers	Brain Hippocampus Middle	brain
25	chr10:52313000-52317000	Enhancers	Brain Anterior Caudate	brain
26	chr10:52313000-52317600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr10:52313000-52319200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr10:52313000-52320600	Weak transcription	HepG2	liver
29	chr10:52313000-52322800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr10:52313200-52333200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr10:52313600-52316800	Enhancers	Left Ventricle	heart
32	chr10:52313600-52317800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr10:52313600-52337400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr10:52313800-52316800	Enhancers	Colon Smooth Muscle	Colon
35	chr10:52313800-52316800	Enhancers	Pancreas	Pancrea
36	chr10:52313800-52320800	Weak transcription	Fetal Kidney	kidney
37	chr10:52314000-52316800	Enhancers	Right Atrium	heart
38	chr10:52314000-52316800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr10:52314200-52316800	Enhancers	Psoas Muscle	Psoas
40	chr10:52314200-52318400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr10:52314400-52316600	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr10:52314600-52316600	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr10:52314600-52316600	Enhancers	Small Intestine	intestine
44	chr10:52314600-52317000	Enhancers	Adipose Nuclei	Adipose
45	chr10:52314600-52317000	Enhancers	Fetal Lung	lung
46	chr10:52314600-52317000	Flanking Active TSS	K562	blood
47	chr10:52314600-52318000	Enhancers	Osteobl	bone
48	chr10:52314600-52318600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr10:52314600-52318600	Enhancers	Rectal Smooth Muscle	rectum
50	chr10:52314600-52319600	Enhancers	NHDF-Ad	bronchial

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