Variant report

Variant	rs3011773
Chromosome Location	chr10:52276085-52276086
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52272048..52276086-chr10:52381938..52384651,3	MCF-7	breast:
2	chr10:52271610..52273554-chr10:52274092..52276247,2	MCF-7	breast:
3	chr10:52268790..52270873-chr10:52275061..52278786,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10508931	0.86[CHB][hapmap]
rs11006190	0.86[CHB][hapmap]
rs11006191	0.86[CHB][hapmap]
rs11006193	0.86[CHB][hapmap]
rs11006194	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs11006197	0.86[CHB][hapmap]
rs11006200	0.86[CHB][hapmap]
rs11006213	0.86[CHB][hapmap]
rs11006233	0.86[CHB][hapmap]
rs11006237	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11006238	0.86[CHB][hapmap]
rs1203375	0.90[CHD][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs1203382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203390	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1203393	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1203395	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1203401	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1203403	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1203405	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1203407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1203409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1203410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1203411	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1203418	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.90[ASN][1000 genomes]
rs1203420	0.90[ASN][1000 genomes]
rs1203421	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs1740761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17496403	0.86[CHB][hapmap]
rs17496500	0.86[CHB][hapmap]
rs1810576	0.96[ASN][1000 genomes]
rs1916567	0.81[CEU][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs2221	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2339402	0.88[ASN][1000 genomes]
rs2574985	0.85[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.85[ASN][1000 genomes]
rs2983347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983350	0.94[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2983354	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2983357	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2983359	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2983361	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2983368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2983369	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2983370	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2983371	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3011770	0.90[CEU][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3011771	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3011779	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3011780	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3011782	0.90[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3011783	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3011786	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3011787	1.00[CEU][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3011788	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3011789	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3011790	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3011791	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3011792	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3011793	0.84[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3011794	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]
rs3011797	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3011801	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7072826	0.86[CHB][hapmap]
rs7921226	0.86[CHB][hapmap]
rs920136	0.85[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[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	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	nsv895391	chr10:52260398-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv895392	chr10:52263910-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv467193	chr10:52265265-52289664	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv550855	chr10:52265265-52289664	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3011773	MSMB	cis	parietal	SCAN
rs3011773	PARG	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52262200-52287200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr10:52266800-52282400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr10:52267000-52282400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr10:52267600-52277800	Enhancers	Brain Anterior Caudate	brain
5	chr10:52268200-52282400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr10:52268200-52282600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr10:52268400-52282200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr10:52268800-52278800	Weak transcription	Primary B cells from cord blood	blood
9	chr10:52270000-52282400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr10:52270000-52282800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr10:52270200-52282600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr10:52271200-52283000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr10:52271600-52276800	Weak transcription	Fetal Lung	lung
14	chr10:52271600-52277400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr10:52271600-52300600	Weak transcription	Aorta	Aorta
16	chr10:52271800-52280800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr10:52272200-52281000	Weak transcription	Fetal Intestine Large	intestine
18	chr10:52272400-52280000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr10:52272400-52280400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr10:52272400-52284600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr10:52272600-52302800	Weak transcription	Fetal Stomach	stomach
22	chr10:52272800-52279000	Weak transcription	Fetal Intestine Small	intestine
23	chr10:52272800-52281200	Weak transcription	Ovary	ovary
24	chr10:52272800-52281400	Weak transcription	Placenta	Placenta
25	chr10:52272800-52281600	Weak transcription	HepG2	liver
26	chr10:52272800-52288200	Weak transcription	HSMMtube	muscle
27	chr10:52273200-52278200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr10:52273200-52278600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr10:52273200-52279000	Weak transcription	Lung	lung
30	chr10:52273200-52281000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr10:52273200-52281600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr10:52273200-52282600	Weak transcription	Right Ventricle	heart
33	chr10:52273200-52285800	Weak transcription	K562	blood
34	chr10:52273200-52287200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr10:52273200-52287400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr10:52273200-52288400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr10:52273400-52278400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr10:52273400-52279000	Weak transcription	Primary B cells from peripheral blood	blood
39	chr10:52273400-52279200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr10:52273400-52281000	Weak transcription	Fetal Muscle Leg	muscle
41	chr10:52273400-52281000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr10:52273400-52281000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr10:52273400-52282600	Weak transcription	Thymus	Thymus
44	chr10:52273400-52282800	Weak transcription	Spleen	Spleen
45	chr10:52273400-52283800	Weak transcription	Fetal Thymus	thymus
46	chr10:52273400-52286000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr10:52273400-52287000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr10:52273400-52287200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr10:52273600-52286800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr10:52273600-52287400	Weak transcription	GM12878-XiMat	blood

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