Variant report

Variant	rs2983357
Chromosome Location	chr10:52301422-52301423
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	chr10:52293246..52296190-chr10:52300383..52302951,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

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];0.89[MKK][hapmap];0.86[AFR][1000 genomes]
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]
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];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1203410	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];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]
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]
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];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2574985	0.84[JPT][hapmap];1.00[MEX][hapmap]
rs2983347	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2983350	0.94[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.96[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];1.00[EUR][1000 genomes];0.97[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];1.00[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];0.96[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];0.84[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];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3011779	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011780	0.98[AMR][1000 genomes];0.98[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];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3011783	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3011786	0.98[AMR][1000 genomes];0.95[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011789	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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];0.96[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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];0.99[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011793	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011794	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]
rs3011797	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];0.97[ASN][1000 genomes]
rs3011801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.91[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
rs2983357	PARG	cis	parietal	SCAN
rs2983357	MSMB	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52272600-52302800	Weak transcription	Fetal Stomach	stomach
2	chr10:52280200-52328000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:52286400-52304000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr10:52287800-52302800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr10:52296800-52302800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr10:52296800-52306000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr10:52297000-52302800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr10:52297000-52304400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr10:52297000-52304600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr10:52297400-52306000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr10:52297800-52302800	Weak transcription	Thymus	Thymus
12	chr10:52298200-52301600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr10:52298200-52301800	Enhancers	Fetal Heart	heart
14	chr10:52298200-52302200	Enhancers	Brain Cingulate Gyrus	brain
15	chr10:52298400-52303400	Enhancers	Primary B cells from peripheral blood	blood
16	chr10:52298600-52302000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr10:52298800-52301600	Weak transcription	Primary T cells from cord blood	blood
18	chr10:52299000-52302800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr10:52299000-52303600	Enhancers	Brain Hippocampus Middle	brain
20	chr10:52299000-52304000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr10:52299000-52304400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr10:52299000-52305400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr10:52299000-52305400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr10:52299000-52310200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr10:52299200-52302600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr10:52299200-52302600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr10:52299200-52302600	Weak transcription	Spleen	Spleen
28	chr10:52299200-52302800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:52299200-52302800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr10:52299200-52302800	Weak transcription	Stomach Mucosa	stomach
31	chr10:52299200-52304000	Weak transcription	Fetal Intestine Small	intestine
32	chr10:52299200-52304600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr10:52299200-52305800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr10:52299200-52310200	Weak transcription	Pancreas	Pancrea
35	chr10:52299400-52302800	Enhancers	K562	blood
36	chr10:52299600-52320600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr10:52299800-52302200	Flanking Active TSS	GM12878-XiMat	blood
38	chr10:52300000-52301600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr10:52300200-52305000	Weak transcription	HepG2	liver
40	chr10:52300400-52301600	Enhancers	Primary T cells fromperipheralblood	blood
41	chr10:52300400-52302200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr10:52300400-52302600	Weak transcription	Brain Angular Gyrus	brain
43	chr10:52300600-52301600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr10:52300600-52301600	Weak transcription	Brain Anterior Caudate	brain
45	chr10:52300600-52301800	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr10:52300600-52302800	Weak transcription	Small Intestine	intestine
47	chr10:52300600-52303200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr10:52300600-52310200	Weak transcription	Placenta	Placenta
49	chr10:52300800-52302000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr10:52300800-52302600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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