Variant report

Variant	rs10254753
Chromosome Location	chr7:6617762-6617763
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:6615537..6618663-chr7:6638717..6641799,3	K562	blood:
2	chr7:6617184..6619983-chr7:6640766..6643695,2	MCF-7	breast:
3	chr7:6615687..6618664-chr7:6627812..6632591,8	MCF-7	breast:
4	chr7:6614342..6622557-chr7:6625132..6631922,18	K562	blood:
5	chr7:6486176..6487864-chr7:6615659..6618201,2	MCF-7	breast:
6	chr6:44214258..44215058-chr7:6617166..6617918,2	Hela-S3	cervix:
7	chr7:6615703..6619364-chr7:6676501..6679314,4	K562	blood:
8	chr16:89988678..89989529-chr7:6617039..6617865,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000146576	Chromatin interaction
ENSG00000259006	Chromatin interaction
ENSG00000164535	Chromatin interaction
ENSG00000232581	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000205903	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10235760	0.94[ASW][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap]
rs10254630	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10255168	0.98[ASN][1000 genomes]
rs10261986	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10273900	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10277061	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10282220	0.95[ASN][1000 genomes]
rs10951988	0.98[ASN][1000 genomes]
rs11559146	1.00[ASN][1000 genomes]
rs11762851	0.86[ASN][1000 genomes]
rs11763814	0.96[ASN][1000 genomes]
rs11770467	0.96[ASN][1000 genomes]
rs12538002	0.93[ASW][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12539700	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12702530	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13226346	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13229391	0.93[ASN][1000 genomes]
rs13229523	0.93[ASN][1000 genomes]
rs13240710	0.88[ASN][1000 genomes]
rs28541711	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088114	0.88[ASW][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap]
rs34060186	0.88[ASN][1000 genomes]
rs34566172	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813513	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075107	0.99[ASN][1000 genomes]
rs4272276	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4512303	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56717970	0.94[ASN][1000 genomes]
rs60108089	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60742375	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62441317	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6963775	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6965187	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7357134	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776724	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790874	0.91[ASN][1000 genomes]
rs7792808	0.93[ASN][1000 genomes]
rs7793367	0.81[ASW][hapmap];0.81[LWK][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7800917	0.88[GIH][hapmap];0.91[MEX][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7801415	0.98[ASN][1000 genomes]
rs7804036	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9640027	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10254753	ZDHHC4	cis	Esophagus Mucosa	GTEx
rs10254753	AC079742.4	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6616000-6617800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr7:6616000-6618000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:6616000-6618000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:6616000-6618000	Active TSS	NHLF	lung
5	chr7:6616200-6617800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr7:6616200-6617800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr7:6616200-6617800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr7:6616200-6617800	Active TSS	A549	lung
9	chr7:6616200-6618200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:6616400-6617800	Active TSS	H1 Cell Line	embryonic stem cell
11	chr7:6616400-6617800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:6616400-6617800	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr7:6616400-6617800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr7:6616400-6617800	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr7:6616400-6617800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr7:6616400-6617800	Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr7:6616400-6617800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:6616400-6617800	Active TSS	Brain Anterior Caudate	brain
19	chr7:6616400-6617800	Active TSS	Brain Hippocampus Middle	brain
20	chr7:6616400-6617800	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr7:6616400-6617800	Active TSS	Brain Substantia Nigra	brain
22	chr7:6616400-6617800	Active TSS	Fetal Intestine Large	intestine
23	chr7:6616400-6617800	Active TSS	Fetal Intestine Small	intestine
24	chr7:6616400-6617800	Active TSS	Fetal Kidney	kidney
25	chr7:6616400-6617800	Active TSS	Fetal Lung	lung
26	chr7:6616400-6617800	Active TSS	Psoas Muscle	Psoas
27	chr7:6616400-6617800	Active TSS	Right Atrium	heart
28	chr7:6616400-6617800	Active TSS	Right Ventricle	heart
29	chr7:6616400-6617800	Active TSS	K562	blood
30	chr7:6616400-6618000	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr7:6616400-6618000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:6616400-6618000	Active TSS	Primary T cells from cord blood	blood
33	chr7:6616400-6618000	Active TSS	Brain Germinal Matrix	brain
34	chr7:6616400-6618000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr7:6616400-6618000	Active TSS	Colon Smooth Muscle	Colon
36	chr7:6616400-6618000	Active TSS	Duodenum Mucosa	Duodenum
37	chr7:6616400-6618000	Active TSS	Hela-S3	cervix
38	chr7:6616400-6618000	Active TSS	HepG2	liver
39	chr7:6616400-6618000	Active TSS	HSMM	muscle
40	chr7:6616400-6618200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr7:6616600-6617800	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr7:6616600-6617800	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr7:6616600-6617800	Active TSS	Dnd41	blood
44	chr7:6616600-6617800	Active TSS	GM12878-XiMat	blood
45	chr7:6616600-6618200	Active TSS	Muscle Satellite Cultured Cells	--
46	chr7:6616600-6618200	Active TSS	Colonic Mucosa	Colon
47	chr7:6617000-6617800	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr7:6617000-6617800	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr7:6617000-6618400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr7:6617200-6617800	Flanking Active TSS	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links