Variant report

Variant	rs3011707
Chromosome Location	chr10:52334588-52334589
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52330729..52340229-chr10:52381715..52386294,12	K562	blood:
2	chr10:52334364..52340801-chr10:52380166..52385556,10	K562	blood:
3	chr10:52333380..52335821-chr10:52336012..52337715,2	K562	blood:
4	chr10:52310656..52316983-chr10:52334408..52339466,9	K562	blood:
5	chr10:52331777..52334924-chr10:52380252..52384970,6	MCF-7	breast:
6	chr10:52318973..52324648-chr10:52334040..52339164,5	K562	blood:

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10763584	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10763585	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10826234	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11006102	0.91[ASN][1000 genomes]
rs11006119	0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11006155	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12358162	0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1884571	0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2208036	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2860472	0.88[JPT][hapmap]
rs2983360	0.83[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2983364	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3011710	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3011802	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3920545	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4935731	0.91[ASN][1000 genomes]
rs4935732	0.91[ASN][1000 genomes]
rs55669848	0.91[ASN][1000 genomes]
rs55735989	0.85[ASN][1000 genomes]
rs56403030	0.91[ASN][1000 genomes]
rs61858108	0.91[ASN][1000 genomes]
rs6481433	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.92[ASN][1000 genomes]
rs7074405	0.93[ASN][1000 genomes]
rs7075104	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7088807	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7898315	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv8660	chr10:52328259-52346278	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3011707	C10orf53	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52308000-52337200	Weak transcription	Primary T cells from cord blood	blood
2	chr10:52311000-52335800	Weak transcription	Esophagus	oesophagus
3	chr10:52312800-52335800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:52312800-52335800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr10:52313600-52337400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr10:52315200-52337400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr10:52315600-52336000	Weak transcription	GM12878-XiMat	blood
8	chr10:52319200-52335800	Weak transcription	Spleen	Spleen
9	chr10:52319600-52335600	Weak transcription	NHEK	skin
10	chr10:52321600-52335600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr10:52321800-52335600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr10:52321800-52335600	Weak transcription	Adipose Nuclei	Adipose
13	chr10:52322000-52335800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr10:52322000-52337200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr10:52322000-52348600	Weak transcription	Fetal Stomach	stomach
16	chr10:52322200-52335600	Weak transcription	NHLF	lung
17	chr10:52322800-52335600	Weak transcription	Fetal Lung	lung
18	chr10:52322800-52336000	Weak transcription	Placenta	Placenta
19	chr10:52324000-52336600	Weak transcription	Thymus	Thymus
20	chr10:52324000-52337400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr10:52324400-52336800	Weak transcription	Primary B cells from cord blood	blood
22	chr10:52324400-52336800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr10:52325400-52336000	Weak transcription	Stomach Mucosa	stomach
24	chr10:52325800-52335200	Weak transcription	Right Ventricle	heart
25	chr10:52325800-52336000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr10:52327400-52336000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr10:52327600-52335800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr10:52328000-52335400	Weak transcription	Fetal Heart	heart
29	chr10:52328600-52336000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:52329800-52335600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr10:52329800-52336600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr10:52329800-52341600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr10:52331200-52334600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr10:52331800-52334600	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr10:52331800-52335600	Weak transcription	Small Intestine	intestine
36	chr10:52332000-52335400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr10:52332000-52336800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr10:52332200-52335800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr10:52332400-52335000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr10:52332400-52335000	Weak transcription	Gastric	stomach
41	chr10:52332400-52335000	Weak transcription	Left Ventricle	heart
42	chr10:52332400-52335000	Weak transcription	Pancreas	Pancrea
43	chr10:52332400-52335200	Weak transcription	Brain Angular Gyrus	brain
44	chr10:52332400-52335400	Weak transcription	Brain Anterior Caudate	brain
45	chr10:52332400-52335400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr10:52332400-52335600	Weak transcription	Psoas Muscle	Psoas
47	chr10:52332400-52335600	Weak transcription	Right Atrium	heart
48	chr10:52332400-52335600	Weak transcription	NHDF-Ad	bronchial
49	chr10:52332400-52335800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr10:52332400-52335800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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