Variant report

Variant	rs11559146
Chromosome Location	chr7:6621277-6621278
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	RUNX3	chr7:6621081-6621871	GM12878	blood:	n/a	n/a
2	RUNX3	chr7:6621133-6621918	GM12878	blood:	n/a	n/a
3	SPI1	chr7:6620997-6621290	GM12878	blood:	n/a	chr7:6621192-6621201
4	BHLHE40	chr7:6621114-6621504	GM12878	blood:	n/a	n/a
5	IKZF1	chr7:6621012-6621806	GM12878	blood:	n/a	n/a
6	MTA3	chr7:6621191-6622005	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6619535..6621612-chr7:6623475..6625158,2	MCF-7	breast:
2	chr7:6614342..6622557-chr7:6625132..6631922,18	K562	blood:
3	chr7:6619810..6621522-chr7:6637808..6639394,2	MCF-7	breast:

Variant related genes	Relation type
ZDHHC4	TF binding region
ENSG00000146576	Chromatin interaction
ENSG00000232581	Chromatin interaction
ENSG00000136247	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10239018	0.92[EUR][1000 genomes]
rs10254630	0.95[ASN][1000 genomes]
rs10254753	1.00[ASN][1000 genomes]
rs10255168	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10273900	1.00[ASN][1000 genomes]
rs10276346	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10277061	1.00[ASN][1000 genomes]
rs10279458	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10282220	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10951987	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10951988	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11762851	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11763814	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11770467	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12532758	0.87[EUR][1000 genomes]
rs12538197	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12669808	0.88[EUR][1000 genomes]
rs12702529	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12702530	0.98[ASN][1000 genomes]
rs13229391	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13229523	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13240710	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1880119	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2346263	0.92[EUR][1000 genomes]
rs28541711	1.00[ASN][1000 genomes]
rs34060186	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34566172	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813513	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4075107	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4272276	0.98[ASN][1000 genomes]
rs4512303	1.00[ASN][1000 genomes]
rs56717970	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59895610	0.86[EUR][1000 genomes]
rs60108089	0.93[ASN][1000 genomes]
rs60742375	0.98[ASN][1000 genomes]
rs62441317	0.88[ASN][1000 genomes]
rs6952785	0.89[EUR][1000 genomes]
rs6965187	0.93[ASN][1000 genomes]
rs73345000	0.85[EUR][1000 genomes]
rs7357134	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776724	1.00[ASN][1000 genomes]
rs7790874	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7790928	0.92[EUR][1000 genomes]
rs7792808	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7793367	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793685	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7800917	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7801415	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7804036	1.00[ASN][1000 genomes]
rs9640027	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
3	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
5	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
6	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
7	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv830895	chr7:6514781-6722092	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	nsv887429	chr7:6520676-6659509	Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv887430	chr7:6520676-6668027	Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv508444	chr7:6534110-6700527	Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv1025220	chr7:6534278-6736802	Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv538717	chr7:6534278-6736802	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
14	nsv887431	chr7:6535517-6690240	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
15	nsv515978	chr7:6535517-6698905	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
16	nsv887432	chr7:6535517-6713985	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
17	nsv887433	chr7:6557135-6668027	Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
18	nsv887434	chr7:6557135-6713985	Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
19	nsv606001	chr7:6563109-6683454	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
20	nsv606002	chr7:6567114-6713985	Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
21	nsv887435	chr7:6613604-6713985	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS 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	32 gene(s)	inside rSNPs	diseases
22	nsv824002	chr7:6618087-6716961	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
23	nsv824003	chr7:6620920-6721409	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11559146	ZDHHC4	cis	parietal	SCAN
rs11559146	ZDHHC4	cis	Esophagus Mucosa	GTEx
rs11559146	GLCCI1	cis	parietal	SCAN
rs11559146	AC079742.4	cis	Esophagus Mucosa	GTEx
rs11559146	NXPH1	cis	cerebellum	SCAN
rs11559146	ZDHHC4	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6617600-6621400	Weak transcription	HSMMtube	muscle
2	chr7:6617600-6621600	Weak transcription	HMEC	breast
3	chr7:6617600-6622400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr7:6617600-6624200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:6617600-6624400	Weak transcription	HUVEC	blood vessel
6	chr7:6617600-6629200	Weak transcription	Small Intestine	intestine
7	chr7:6617600-6629600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:6617600-6629800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr7:6617600-6630000	Weak transcription	Stomach Mucosa	stomach
10	chr7:6617800-6621400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr7:6617800-6621800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr7:6617800-6623000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:6617800-6623000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr7:6617800-6629000	Weak transcription	Right Atrium	heart
15	chr7:6617800-6629200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr7:6618000-6622600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr7:6618200-6622600	Weak transcription	Fetal Heart	heart
18	chr7:6618200-6626800	Strong transcription	Brain Hippocampus Middle	brain
19	chr7:6618200-6628800	Weak transcription	Fetal Brain Male	brain
20	chr7:6618200-6629000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr7:6618200-6629000	Strong transcription	Brain Cingulate Gyrus	brain
22	chr7:6618200-6629200	Strong transcription	Fetal Intestine Small	intestine
23	chr7:6618400-6621400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr7:6618400-6622400	Weak transcription	Colonic Mucosa	Colon
25	chr7:6618400-6628800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr7:6618400-6628800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr7:6618400-6629000	Strong transcription	Fetal Muscle Leg	muscle
28	chr7:6618400-6629000	Strong transcription	Fetal Thymus	thymus
29	chr7:6618600-6621600	Weak transcription	A549	lung
30	chr7:6618600-6629000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr7:6618600-6629000	Strong transcription	Fetal Stomach	stomach
32	chr7:6618800-6628600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:6618800-6628600	Strong transcription	Liver	Liver
34	chr7:6618800-6629000	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr7:6619000-6625400	Strong transcription	Thymus	Thymus
36	chr7:6619000-6625600	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr7:6619000-6626200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr7:6619000-6626800	Strong transcription	Brain Anterior Caudate	brain
39	chr7:6619000-6627000	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr7:6619000-6628600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr7:6619200-6628800	Strong transcription	Fetal Intestine Large	intestine
42	chr7:6619200-6629000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr7:6619200-6629000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr7:6619400-6622200	Strong transcription	K562	blood
45	chr7:6619600-6625200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr7:6619600-6629000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr7:6619800-6623600	Strong transcription	NHEK	skin
48	chr7:6619800-6626200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr7:6619800-6626400	Strong transcription	Brain Germinal Matrix	brain
50	chr7:6619800-6627400	Strong transcription	Rectal Mucosa Donor 29	rectum

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