Variant report

Variant	rs12555
Chromosome Location	chr7:56130832-56130833
allele	A/T
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	POLR2A	chr7:56130473-56130840	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr7:56129753-56130858	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:56130230-56130900	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr7:56129473-56132306	HepG2	liver:	n/a	n/a
5	POLR2A	chr7:56130055-56130925	GM12892	blood:	n/a	n/a
6	POLR2A	chr7:56130453-56130837	GM12892	blood:	n/a	n/a
7	POLR2A	chr7:56129176-56132427	H1-hESC	embryonic stem cell:	n/a	n/a
8	JUND	chr7:56129561-56132335	K562	blood:	n/a	chr7:56130289-56130299 chr7:56130288-56130300 chr7:56130290-56130299 chr7:56130291-56130298 chr7:56130288-56130299 chr7:56130290-56130298 chr7:56131888-56131897
9	POLR2A	chr7:56130532-56132548	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr7:56130015-56131061	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr7:56130337-56130908	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:56128361..56131760-chr7:56167519..56170434,3	K562	blood:
2	chr7:56117123..56123487-chr7:56128716..56133468,11	MCF-7	breast:
3	chr7:56018165..56022272-chr7:56129856..56132253,4	K562	blood:
4	chr7:56126631..56129395-chr7:56129953..56133299,4	MCF-7	breast:
5	chr7:56124986..56128195-chr7:56129879..56132286,4	MCF-7	breast:
6	chr7:56018384..56020889-chr7:56129856..56132224,2	K562	blood:
7	chr7:56031002..56032516-chr7:56130202..56131906,2	K562	blood:
8	chr7:56130207..56133425-chr7:56142360..56145052,4	K562	blood:

Variant related genes	Relation type
SUMF2	TF binding region
ENSG00000146729	Chromatin interaction
ENSG00000146733	Chromatin interaction
ENSG00000129103	Chromatin interaction
ENSG00000206603	Chromatin interaction
ENSG00000238673	Chromatin interaction
ENSG00000239789	Chromatin interaction
ENSG00000146731	Chromatin interaction
ENSG00000207168	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10085802	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253539	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253680	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13223519	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229704	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13232704	0.80[EUR][1000 genomes]
rs13233037	0.80[EUR][1000 genomes]
rs13233834	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13234504	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238029	1.00[EUR][1000 genomes]
rs13238083	0.80[EUR][1000 genomes]
rs13240361	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13241531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13247558	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151447	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013197	0.81[ASN][1000 genomes]
rs2304375	0.85[ASN][1000 genomes]
rs2331184	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33922584	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34023503	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34154824	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34319969	1.00[ASN][1000 genomes]
rs34334997	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34573211	0.96[EUR][1000 genomes]
rs34822782	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35007015	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35033933	1.00[EUR][1000 genomes]
rs35058595	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35102507	1.00[EUR][1000 genomes]
rs35136814	0.92[ASN][1000 genomes]
rs35347055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35506072	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35515485	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35523043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35581685	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35818005	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35881493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36044787	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36049923	1.00[ASN][1000 genomes]
rs36148650	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778868	1.00[ASN][1000 genomes]
rs4947531	0.82[ASN][1000 genomes]
rs4948089	0.82[ASN][1000 genomes]
rs4948101	0.92[ASN][1000 genomes]
rs71543774	0.80[EUR][1000 genomes]
rs71543775	0.92[ASN][1000 genomes]
rs71543776	0.89[ASN][1000 genomes]
rs71543777	0.92[ASN][1000 genomes]
rs71543786	1.00[EUR][1000 genomes]
rs73126344	1.00[ASN][1000 genomes]
rs816219	0.83[ASN][1000 genomes]
rs816242	0.96[ASN][1000 genomes]
rs816412	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816413	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816415	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv981474	chr7:56127123-56131412	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56120200-56131200	Weak transcription	Aorta	Aorta
2	chr7:56120600-56131000	Strong transcription	Adipose Nuclei	Adipose
3	chr7:56120800-56131200	Strong transcription	Fetal Thymus	thymus
4	chr7:56120800-56131400	Strong transcription	Fetal Muscle Leg	muscle
5	chr7:56120800-56131600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:56121000-56131000	Strong transcription	Brain Anterior Caudate	brain
7	chr7:56121000-56131200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr7:56121000-56131200	Strong transcription	Brain Hippocampus Middle	brain
9	chr7:56121200-56131200	Strong transcription	Brain Germinal Matrix	brain
10	chr7:56121200-56131200	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr7:56121200-56131400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr7:56121200-56131400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr7:56121400-56131000	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr7:56121400-56131000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr7:56121400-56131000	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr7:56121400-56131200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr7:56121400-56131200	Strong transcription	Placenta	Placenta
18	chr7:56121400-56131200	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr7:56121400-56131200	Genic enhancers	Dnd41	blood
20	chr7:56121400-56131400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr7:56121400-56131400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr7:56121600-56131000	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr7:56121600-56131000	Strong transcription	Stomach Smooth Muscle	stomach
24	chr7:56121600-56131200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:56121600-56131200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr7:56121600-56131200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr7:56121800-56131400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:56122000-56131200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr7:56122000-56131200	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr7:56122000-56131400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr7:56122400-56131400	Strong transcription	Fetal Brain Female	brain
32	chr7:56122600-56131400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr7:56122600-56131400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr7:56122800-56131200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr7:56123200-56131200	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr7:56123600-56131000	Strong transcription	Primary T cells from cord blood	blood
37	chr7:56123600-56131200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr7:56124800-56131600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr7:56125800-56131000	Weak transcription	Pancreas	Pancrea
40	chr7:56126000-56131000	Weak transcription	Gastric	stomach
41	chr7:56126800-56131400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:56127000-56132000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr7:56127400-56131200	Strong transcription	Colon Smooth Muscle	Colon
44	chr7:56127400-56131600	Genic enhancers	Fetal Intestine Large	intestine
45	chr7:56127600-56131400	Weak transcription	Spleen	Spleen
46	chr7:56127600-56131600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr7:56127800-56131800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr7:56128000-56131200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr7:56128000-56131400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr7:56128000-56131600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood

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