Variant report

Variant	rs12668193
Chromosome Location	chr7:56172378-56172379
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56047807..56050319-chr7:56171893..56174174,2	K562	blood:
2	chr7:56171801..56173788-chr7:56307425..56310338,2	K562	blood:

Variant related genes	Relation type
ENSG00000146729	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10265826	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10274148	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10800	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12154781	0.81[AMR][1000 genomes]
rs12155441	0.81[AMR][1000 genomes]
rs12536548	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12537948	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12671494	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12673255	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13438048	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2014042	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2242509	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2270244	0.81[AFR][1000 genomes]
rs28438587	0.81[AMR][1000 genomes]
rs28558245	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3778867	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3813505	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4345511	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4424212	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4427122	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4585698	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55940597	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56355538	0.82[AFR][1000 genomes]
rs58251663	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59723101	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6947671	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6960348	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6970842	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6971804	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73140779	0.86[AFR][1000 genomes]
rs73140793	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73140794	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs766334	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7793536	0.82[EUR][1000 genomes]
rs7793614	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv1034712	chr7:56146885-56605592	Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
12	nsv538861	chr7:56146885-56605592	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
13	nsv970483	chr7:56169231-56172955	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv526294	chr7:56171489-56622630	Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12668193	SUMF2	cis	lung	GTEx
rs12668193	SUMF2	cis	Esophagus Muscularis	GTEx
rs12668193	SUMF2	cis	Whole Blood	GTEx
rs12668193	SUMF2	cis	Artery Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56158200-56173200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:56161000-56173000	Weak transcription	Fetal Heart	heart
3	chr7:56161200-56173000	Weak transcription	Right Atrium	heart
4	chr7:56164000-56172800	Strong transcription	Fetal Stomach	stomach
5	chr7:56164200-56172600	Strong transcription	Fetal Intestine Small	intestine
6	chr7:56165200-56172800	Strong transcription	Thymus	Thymus
7	chr7:56165400-56172400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:56166200-56172600	Strong transcription	Fetal Muscle Leg	muscle
9	chr7:56167000-56172600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr7:56167000-56172800	Strong transcription	A549	lung
11	chr7:56167000-56173200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr7:56167200-56172400	Strong transcription	Fetal Lung	lung
13	chr7:56167200-56172800	Strong transcription	NHEK	skin
14	chr7:56167400-56172600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:56167400-56172800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:56167600-56173200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr7:56169000-56173200	Weak transcription	Esophagus	oesophagus
18	chr7:56170000-56173000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:56170800-56173000	Weak transcription	Fetal Kidney	kidney
20	chr7:56171400-56172400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:56171400-56172600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
22	chr7:56171400-56172600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr7:56171600-56172800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr7:56171600-56173000	Weak transcription	Brain Germinal Matrix	brain
25	chr7:56171800-56172400	Genic enhancers	Stomach Smooth Muscle	stomach
26	chr7:56171800-56172600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:56171800-56172600	Weak transcription	Fetal Brain Male	brain
28	chr7:56171800-56172600	Weak transcription	Stomach Mucosa	stomach
29	chr7:56171800-56172800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr7:56171800-56172800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:56171800-56172800	Weak transcription	Brain Angular Gyrus	brain
32	chr7:56171800-56173000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr7:56171800-56173000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr7:56172000-56172400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:56172000-56172600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:56172000-56172600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr7:56172000-56172600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr7:56172000-56172600	Weak transcription	Liver	Liver
39	chr7:56172000-56172600	Weak transcription	Brain Hippocampus Middle	brain
40	chr7:56172000-56172600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr7:56172000-56172600	Weak transcription	Lung	lung
42	chr7:56172000-56172600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr7:56172000-56172600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr7:56172000-56172600	Weak transcription	Small Intestine	intestine
45	chr7:56172000-56172600	Genic enhancers	Dnd41	blood
46	chr7:56172000-56172600	Weak transcription	HMEC	breast
47	chr7:56172000-56172800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr7:56172000-56172800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr7:56172000-56172800	Weak transcription	Primary B cells from cord blood	blood
50	chr7:56172000-56172800	Weak transcription	Primary B cells from peripheral blood	blood

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