Variant report

Variant	rs12708257
Chromosome Location	chr9:14689633-14689634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:14686674..14691236-chr9:14691548..14694778,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175893	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10119411	0.85[CEU][hapmap]
rs10511594	0.91[CHB][hapmap]
rs10756594	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10810212	0.83[CHB][hapmap]
rs10961651	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs10961652	0.91[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs10961653	0.91[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10961654	0.91[ASN][1000 genomes]
rs10961655	0.91[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs11562183	0.87[ASN][1000 genomes]
rs12551707	0.84[CHB][hapmap]
rs12554698	0.84[CHB][hapmap]
rs13284901	1.00[CHB][hapmap]
rs13289971	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs13290219	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs13296430	0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17288444	0.95[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4469563	0.81[ASN][1000 genomes]
rs7849480	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv831517	chr9:14512924-14738206	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv613637	chr9:14524438-15011915	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3362157	chr9:14542189-14791977	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv521363	chr9:14566406-14691897	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv892605	chr9:14585052-14709151	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv892606	chr9:14588049-14697022	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv892609	chr9:14589173-14694302	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv2752921	chr9:14593749-14694372	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv892612	chr9:14654900-14694302	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv892613	chr9:14657139-14694302	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv6482	chr9:14673695-14718568	Enhancers Strong transcription ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv3513870	chr9:14686102-14689700	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv3513871	chr9:14686102-14689700	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv1025566	chr9:14687088-14791199	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv613645	chr9:14687455-14690419	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12708257	ZDHHC21	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14631000-14692400	Weak transcription	HSMMtube	muscle
2	chr9:14634600-14692400	Weak transcription	Gastric	stomach
3	chr9:14634600-14692600	Weak transcription	Aorta	Aorta
4	chr9:14654200-14692600	Weak transcription	Pancreas	Pancrea
5	chr9:14655200-14690600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:14655400-14690600	Weak transcription	Brain Angular Gyrus	brain
7	chr9:14655400-14690600	Weak transcription	Fetal Kidney	kidney
8	chr9:14655400-14691000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:14655400-14691400	Weak transcription	A549	lung
10	chr9:14655400-14692200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr9:14655600-14692200	Weak transcription	Fetal Lung	lung
12	chr9:14655800-14692200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:14656000-14692400	Weak transcription	Colonic Mucosa	Colon
14	chr9:14656200-14692400	Weak transcription	Primary T cells from cord blood	blood
15	chr9:14657000-14692600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:14659600-14692400	Weak transcription	Colon Smooth Muscle	Colon
17	chr9:14660200-14691000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr9:14663400-14692000	Weak transcription	Brain Substantia Nigra	brain
19	chr9:14670800-14692200	Weak transcription	NHLF	lung
20	chr9:14671200-14692000	Weak transcription	HepG2	liver
21	chr9:14671600-14692200	Weak transcription	NHEK	skin
22	chr9:14672600-14692400	Weak transcription	Small Intestine	intestine
23	chr9:14672800-14692200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr9:14675400-14692400	Weak transcription	Ovary	ovary
25	chr9:14676800-14692200	Weak transcription	Fetal Brain Female	brain
26	chr9:14678400-14690800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr9:14678800-14692200	Weak transcription	Liver	Liver
28	chr9:14679200-14691000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:14680200-14692200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr9:14681400-14690400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr9:14681400-14692600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:14681800-14691000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr9:14681800-14692200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:14682000-14692600	Weak transcription	Spleen	Spleen
35	chr9:14685000-14692400	Weak transcription	Right Ventricle	heart
36	chr9:14685800-14690200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr9:14685800-14690400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:14685800-14690400	Strong transcription	Fetal Muscle Leg	muscle
39	chr9:14685800-14691000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:14685800-14692400	Weak transcription	Thymus	Thymus
41	chr9:14686000-14690400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:14686200-14690200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr9:14686200-14690400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:14686200-14690400	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr9:14686200-14690400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr9:14686200-14690800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:14686200-14691000	Weak transcription	Dnd41	blood
48	chr9:14686200-14692400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr9:14686400-14690000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr9:14686400-14690000	Strong transcription	Fetal Intestine Small	intestine

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