Variant report

Variant	rs17497064
Chromosome Location	chr10:52368525-52368526
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52366580..52370875-chr10:52371309..52374318,4	K562	blood:
2	chr10:52367499..52369355-chr10:52371590..52373670,2	MCF-7	breast:
3	chr10:52367316..52369194-chr10:52370537..52372396,2	MCF-7	breast:
4	chr10:52367696..52369348-chr10:52383415..52385281,2	MCF-7	breast:
5	chr10:52365691..52371767-chr10:52381261..52385919,7	K562	blood:
6	chr10:52363969..52366872-chr10:52366929..52369870,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230036	Chromatin interaction
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11006259	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11006281	0.94[ASN][1000 genomes]
rs3001879	0.92[ASN][1000 genomes]
rs3001883	0.92[ASN][1000 genomes]
rs3001885	0.92[ASN][1000 genomes]
rs3011714	0.92[ASN][1000 genomes]
rs4268459	0.94[ASN][1000 genomes]
rs4935734	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4935735	0.94[ASN][1000 genomes]
rs4935737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4935738	0.84[AFR][1000 genomes]
rs4935739	0.94[ASN][1000 genomes]
rs6481442	0.96[ASN][1000 genomes]
rs6481461	0.92[ASN][1000 genomes]
rs7067552	0.96[ASN][1000 genomes]
rs7073182	0.90[ASN][1000 genomes]
rs7089882	0.87[ASN][1000 genomes]
rs7090996	0.94[ASN][1000 genomes]
rs7094655	0.96[ASN][1000 genomes]
rs7904101	0.94[ASN][1000 genomes]
rs7908136	0.93[ASN][1000 genomes]
rs7909486	0.95[ASN][1000 genomes]
rs7918559	0.84[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17497064	FLJ31958	N/A	lymphoblastoid	RTeQTL
rs17497064	RP11-564C4.6	cis	Thyroid	GTEx
rs17497064	RP11-564C4.6	cis	Whole Blood	GTEx
rs17497064	FLJ31958	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52341200-52373000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr10:52359400-52369200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr10:52360200-52375600	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr10:52361600-52369000	Enhancers	Brain Anterior Caudate	brain
5	chr10:52362200-52372400	Weak transcription	Esophagus	oesophagus
6	chr10:52362600-52368800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr10:52363200-52371600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr10:52363200-52372000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr10:52364000-52369800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr10:52364200-52370000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr10:52364400-52372000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr10:52364400-52374400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr10:52365000-52368800	Enhancers	Fetal Heart	heart
14	chr10:52365000-52368800	Weak transcription	Thymus	Thymus
15	chr10:52365000-52369800	Weak transcription	Gastric	stomach
16	chr10:52365000-52369800	Weak transcription	Right Atrium	heart
17	chr10:52365000-52371000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr10:52365200-52369600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr10:52365200-52374000	Weak transcription	Placenta	Placenta
20	chr10:52365400-52369000	Enhancers	Liver	Liver
21	chr10:52365400-52370200	Weak transcription	Fetal Thymus	thymus
22	chr10:52365400-52370200	Weak transcription	Spleen	Spleen
23	chr10:52365400-52370800	Weak transcription	Lung	lung
24	chr10:52365400-52371200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr10:52365400-52371200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr10:52365400-52371400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr10:52365400-52375000	Weak transcription	Fetal Brain Female	brain
28	chr10:52365400-52379400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr10:52365600-52370600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr10:52365600-52372000	Weak transcription	Fetal Kidney	kidney
31	chr10:52365600-52377200	Weak transcription	Primary T cells from cord blood	blood
32	chr10:52365800-52372400	Weak transcription	Fetal Intestine Small	intestine
33	chr10:52365800-52378200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr10:52366000-52373000	Weak transcription	Fetal Intestine Large	intestine
35	chr10:52366000-52381600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr10:52366600-52370800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr10:52366600-52372600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr10:52366600-52377800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr10:52367200-52368600	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr10:52367200-52369600	Weak transcription	Left Ventricle	heart
41	chr10:52367200-52369600	Weak transcription	Right Ventricle	heart
42	chr10:52367200-52377800	Weak transcription	Primary B cells from cord blood	blood
43	chr10:52367200-52379400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr10:52367400-52369600	Weak transcription	Brain Angular Gyrus	brain
45	chr10:52367400-52369600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr10:52367400-52369600	Weak transcription	Psoas Muscle	Psoas
47	chr10:52367400-52381400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr10:52367600-52369600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr10:52367600-52371600	Weak transcription	Fetal Brain Male	brain
50	chr10:52367600-52372000	Weak transcription	GM12878-XiMat	blood

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