Variant report

Variant	rs17688516
Chromosome Location	chr6:27328577-27328578
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	ZNF274	chr6:27325382-27328798	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27177161..27179137-chr6:27326485..27328754,2	K562	blood:

Variant related genes	Relation type
ZNF204P	TF binding region
ENSG00000174572	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1127574	0.98[ASN][1000 genomes]
rs12199213	0.98[ASN][1000 genomes]
rs12213055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1555040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17739702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17739727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2064092	0.88[JPT][hapmap]
rs55923531	0.89[ASN][1000 genomes]
rs62622793	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72839482	0.91[ASN][1000 genomes]
rs764285	0.85[ASN][1000 genomes]
rs9461362	1.00[JPT][hapmap]
rs9461363	0.88[ASN][1000 genomes]
rs9461366	0.85[ASN][1000 genomes]
rs9468076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9468149	0.88[JPT][hapmap]
rs9468152	0.88[JPT][hapmap]
rs9468153	0.89[JPT][hapmap]
rs9468155	0.89[JPT][hapmap]
rs9468159	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17688516	ZNF204P	cis	Muscle Skeletal	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27316800-27335400	Weak transcription	Pancreas	Pancrea
2	chr6:27325800-27336200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:27326000-27331200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
4	chr6:27326000-27335600	Weak transcription	Brain Germinal Matrix	brain
5	chr6:27326200-27331000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:27326400-27329600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
7	chr6:27326400-27331800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:27326600-27328800	ZNF genes & repeats	Fetal Lung	lung
9	chr6:27326600-27329400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
10	chr6:27326800-27330800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
11	chr6:27326800-27331200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:27326800-27342000	Weak transcription	Colonic Mucosa	Colon
13	chr6:27327000-27328600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:27327000-27329200	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:27327000-27332000	Weak transcription	Stomach Mucosa	stomach
16	chr6:27327000-27342000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:27327400-27329600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
18	chr6:27327400-27330200	Weak transcription	Brain Anterior Caudate	brain
19	chr6:27327400-27333400	Weak transcription	Aorta	Aorta
20	chr6:27327400-27335600	Weak transcription	Gastric	stomach
21	chr6:27327400-27335800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:27327400-27336600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:27327400-27341800	Weak transcription	Fetal Brain Male	brain
24	chr6:27327400-27341800	Weak transcription	Fetal Kidney	kidney
25	chr6:27327600-27328800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr6:27327600-27329800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:27327600-27335800	Weak transcription	Brain Angular Gyrus	brain
28	chr6:27327600-27342200	Weak transcription	Brain Substantia Nigra	brain
29	chr6:27327800-27329800	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr6:27328000-27328600	Weak transcription	Left Ventricle	heart
31	chr6:27328000-27328800	Weak transcription	Ovary	ovary
32	chr6:27328000-27335600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr6:27328000-27342400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:27328200-27328800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr6:27328200-27329000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:27328200-27329200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr6:27328200-27330200	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:27328200-27330600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr6:27328200-27335800	Weak transcription	Right Ventricle	heart
40	chr6:27328200-27341800	Weak transcription	Adipose Nuclei	Adipose
41	chr6:27328200-27341800	Weak transcription	Brain Hippocampus Middle	brain
42	chr6:27328200-27341800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:27328200-27342200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:27328400-27335200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:27328400-27341800	Weak transcription	Rectal Mucosa Donor 31	rectum

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