Variant report

Variant	rs13229523
Chromosome Location	chr7:6649610-6649611
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	chr7:6649329..6651399-chr7:6652543..6654507,2	MCF-7	breast:
2	chr7:6629736..6633407-chr7:6648974..6652007,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146576	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10239018	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10254630	0.97[ASN][1000 genomes]
rs10254753	0.93[ASN][1000 genomes]
rs10255168	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10273900	0.93[ASN][1000 genomes]
rs10276346	0.87[EUR][1000 genomes]
rs10277061	0.93[ASN][1000 genomes]
rs10279458	0.85[EUR][1000 genomes]
rs10282220	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10951987	0.87[EUR][1000 genomes]
rs10951988	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11559146	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11762851	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11763814	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11763918	0.81[ASN][1000 genomes]
rs11770467	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12532758	0.85[EUR][1000 genomes]
rs12538197	0.88[EUR][1000 genomes]
rs12669808	0.86[EUR][1000 genomes]
rs12702529	0.83[EUR][1000 genomes]
rs12702530	0.96[ASN][1000 genomes]
rs13229391	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13240710	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1880119	0.88[EUR][1000 genomes]
rs2346263	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28541711	0.93[ASN][1000 genomes]
rs34060186	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34566172	0.93[ASN][1000 genomes]
rs3813513	0.93[ASN][1000 genomes]
rs4075107	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4272276	0.96[ASN][1000 genomes]
rs4512303	0.93[ASN][1000 genomes]
rs56717970	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59895610	0.84[EUR][1000 genomes]
rs60108089	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60742375	0.91[ASN][1000 genomes]
rs62441317	0.92[ASN][1000 genomes]
rs6952785	0.87[EUR][1000 genomes]
rs6965187	1.00[ASN][1000 genomes]
rs73345000	0.82[EUR][1000 genomes]
rs7357134	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7776724	0.93[ASN][1000 genomes]
rs7790874	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7790928	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7792808	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7793367	0.93[ASN][1000 genomes]
rs7793685	0.85[EUR][1000 genomes]
rs7800917	0.93[ASN][1000 genomes]
rs7801415	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7804036	0.93[ASN][1000 genomes]
rs9640027	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	nsv887436	chr7:6626922-6721661	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Enhancers Bivalent/Poised TSS 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
22	esv1797143	chr7:6628177-6705439	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
23	nsv606003	chr7:6628242-6713985	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
24	nsv606004	chr7:6643664-6692573	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
25	nsv887437	chr7:6645281-6704332	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13229523	ZDHHC4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6631400-6649800	Strong transcription	Fetal Intestine Small	intestine
2	chr7:6631400-6649800	Strong transcription	Fetal Stomach	stomach
3	chr7:6631600-6650800	Strong transcription	Thymus	Thymus
4	chr7:6632000-6650600	Strong transcription	Brain Germinal Matrix	brain
5	chr7:6636000-6654600	Weak transcription	Psoas Muscle	Psoas
6	chr7:6637800-6653000	Weak transcription	HMEC	breast
7	chr7:6637800-6653200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:6640600-6653400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr7:6642000-6654400	Weak transcription	Colon Smooth Muscle	Colon
10	chr7:6642000-6654400	Weak transcription	Fetal Brain Male	brain
11	chr7:6642400-6651800	Weak transcription	K562	blood
12	chr7:6642400-6654600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr7:6642600-6650000	Weak transcription	NH-A	brain
14	chr7:6642600-6650600	Weak transcription	NHDF-Ad	bronchial
15	chr7:6642600-6650800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr7:6642600-6653600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr7:6642600-6654400	Weak transcription	Fetal Kidney	kidney
18	chr7:6642600-6654400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr7:6642600-6654600	Weak transcription	Brain Angular Gyrus	brain
20	chr7:6642800-6652400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr7:6642800-6654600	Weak transcription	HSMM	muscle
22	chr7:6643600-6653400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr7:6644000-6652000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr7:6644200-6653600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr7:6644200-6653600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:6644400-6654400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr7:6644400-6654400	Weak transcription	Brain Substantia Nigra	brain
28	chr7:6644600-6650400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr7:6644600-6650800	Weak transcription	NHEK	skin
30	chr7:6644600-6651200	Weak transcription	GM12878-XiMat	blood
31	chr7:6644600-6653600	Weak transcription	HepG2	liver
32	chr7:6644600-6654400	Weak transcription	Fetal Lung	lung
33	chr7:6644800-6654400	Weak transcription	Ovary	ovary
34	chr7:6645200-6654200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr7:6645800-6654200	Weak transcription	Primary B cells from cord blood	blood
36	chr7:6646000-6649800	Weak transcription	HSMMtube	muscle
37	chr7:6646000-6650600	Weak transcription	A549	lung
38	chr7:6646200-6654400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr7:6646400-6652200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr7:6646600-6653400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr7:6646600-6654400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr7:6647400-6654400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr7:6648000-6654400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr7:6648200-6651000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:6648200-6651200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr7:6648200-6652400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr7:6648200-6654200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr7:6648200-6654400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr7:6648200-6654400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr7:6648200-6654400	Weak transcription	Brain Hippocampus Middle	brain

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