Variant report

Variant	rs9568664
Chromosome Location	chr13:52354491-52354492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:52354369-52354646	HepG2	liver:	n/a	n/a
2	STAT3	chr13:52354432-52354813	MCF10A-Er-Src	breast:	n/a	chr13:52354641-52354650 chr13:52354453-52354460 chr13:52354640-52354649

No.	Distal block	Cell Line	Cell type
1	chr13:52353786..52355970-chr13:52358653..52360551,2	K562	blood:
2	chr13:52352368..52355270-chr13:52370453..52372078,2	MCF-7	breast:
3	chr13:52022276..52028052-chr13:52350866..52359408,15	MCF-7	breast:
4	chr13:52354470..52357253-chr13:52359051..52361790,2	K562	blood:
5	chr13:51986391..51989343-chr13:52354018..52356023,2	MCF-7	breast:

Variant related genes	Relation type
DHRS12	TF binding region
ENSG00000102786	Chromatin interaction
ENSG00000236778	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs9568640	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers 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
9	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	esv1840020	chr13:52345838-52388765	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9568664	NEK3	cis	lymphoblastoid	seeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52330600-52355600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:52339400-52356200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr13:52339400-52357400	Weak transcription	Colonic Mucosa	Colon
4	chr13:52339600-52356800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr13:52339600-52361400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr13:52339600-52375000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr13:52339800-52359800	Weak transcription	Colon Smooth Muscle	Colon
8	chr13:52339800-52371400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr13:52339800-52375200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr13:52341400-52354600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr13:52341400-52361200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr13:52341600-52356400	Weak transcription	Brain Germinal Matrix	brain
13	chr13:52342600-52356200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr13:52342800-52355800	Weak transcription	Primary B cells from cord blood	blood
15	chr13:52343800-52360200	Weak transcription	Small Intestine	intestine
16	chr13:52344200-52357800	Weak transcription	HSMM	muscle
17	chr13:52344600-52355400	Weak transcription	Spleen	Spleen
18	chr13:52344600-52371800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr13:52344800-52355600	Weak transcription	Right Ventricle	heart
20	chr13:52344800-52359600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr13:52344800-52360000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr13:52344800-52360000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr13:52345400-52355600	Weak transcription	HepG2	liver
24	chr13:52345400-52363400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr13:52345600-52359600	Weak transcription	Lung	lung
26	chr13:52345800-52355600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr13:52346200-52355400	Weak transcription	Left Ventricle	heart
28	chr13:52346200-52355600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr13:52346200-52357800	Weak transcription	Primary T cells from cord blood	blood
30	chr13:52346400-52355800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr13:52346400-52356200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr13:52346400-52376000	Weak transcription	Thymus	Thymus
33	chr13:52347800-52355600	Weak transcription	Right Atrium	heart
34	chr13:52348000-52360000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr13:52348000-52360200	Weak transcription	Fetal Intestine Large	intestine
36	chr13:52348000-52361000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr13:52348200-52355600	Weak transcription	Ovary	ovary
38	chr13:52348200-52356400	Weak transcription	Liver	Liver
39	chr13:52348200-52359600	Weak transcription	Brain Anterior Caudate	brain
40	chr13:52348200-52360200	Weak transcription	Aorta	Aorta
41	chr13:52348200-52361400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr13:52348200-52362600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr13:52348200-52375600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr13:52348200-52375600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr13:52350600-52355400	Weak transcription	Gastric	stomach
46	chr13:52350600-52360200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr13:52350600-52367200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr13:52351400-52356400	Weak transcription	Fetal Intestine Small	intestine
49	chr13:52351600-52355600	Weak transcription	Adipose Nuclei	Adipose
50	chr13:52352200-52355600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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