Variant report

Variant	rs13238029
Chromosome Location	chr7:56125349-56125350
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	POLR2A	chr7:56124712-56125371	K562	blood:	n/a	n/a
2	POLR2A	chr7:56125150-56125597	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:56124950-56126074	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr7:56124935-56125405	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr7:56124894-56125487	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56124986..56128195-chr7:56129879..56132286,4	MCF-7	breast:

Variant related genes	Relation type
CCT6A	TF binding region
SNORA15	TF binding region
ENSG00000129103	Chromatin interaction
ENSG00000146731	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10085802	0.92[EUR][1000 genomes]
rs10253539	0.92[EUR][1000 genomes]
rs10253680	0.92[EUR][1000 genomes]
rs12555	1.00[EUR][1000 genomes]
rs13223519	0.82[EUR][1000 genomes]
rs13229704	1.00[EUR][1000 genomes]
rs13232704	0.80[EUR][1000 genomes]
rs13233037	0.80[EUR][1000 genomes]
rs13233834	1.00[EUR][1000 genomes]
rs13234504	1.00[EUR][1000 genomes]
rs13238083	0.80[EUR][1000 genomes]
rs13240361	1.00[EUR][1000 genomes]
rs13241531	0.91[EUR][1000 genomes]
rs13245395	1.00[AMR][1000 genomes]
rs13247558	1.00[EUR][1000 genomes]
rs17151447	1.00[EUR][1000 genomes]
rs2331184	0.85[EUR][1000 genomes]
rs33922584	0.96[EUR][1000 genomes]
rs34023503	0.91[EUR][1000 genomes]
rs34154824	1.00[EUR][1000 genomes]
rs34334997	0.96[EUR][1000 genomes]
rs34573211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34822782	0.92[EUR][1000 genomes]
rs35007015	0.92[EUR][1000 genomes]
rs35033933	1.00[EUR][1000 genomes]
rs35058595	0.83[EUR][1000 genomes]
rs35102507	1.00[EUR][1000 genomes]
rs35347055	0.92[EUR][1000 genomes]
rs35506072	1.00[EUR][1000 genomes]
rs35515485	1.00[EUR][1000 genomes]
rs35523043	1.00[EUR][1000 genomes]
rs35581685	1.00[EUR][1000 genomes]
rs35818005	1.00[EUR][1000 genomes]
rs35881493	1.00[EUR][1000 genomes]
rs36044787	1.00[EUR][1000 genomes]
rs36148650	1.00[EUR][1000 genomes]
rs71543774	0.80[EUR][1000 genomes]
rs71543786	1.00[EUR][1000 genomes]
rs816412	0.92[EUR][1000 genomes]
rs816413	0.92[EUR][1000 genomes]
rs816415	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56120200-56125600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:56120200-56131200	Weak transcription	Aorta	Aorta
3	chr7:56120600-56131000	Strong transcription	Adipose Nuclei	Adipose
4	chr7:56120800-56127400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:56120800-56130000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr7:56120800-56130400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:56120800-56130800	Strong transcription	Brain Angular Gyrus	brain
8	chr7:56120800-56131200	Strong transcription	Fetal Thymus	thymus
9	chr7:56120800-56131400	Strong transcription	Fetal Muscle Leg	muscle
10	chr7:56120800-56131600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:56121000-56130000	Weak transcription	Stomach Mucosa	stomach
12	chr7:56121000-56130800	Strong transcription	Fetal Lung	lung
13	chr7:56121000-56131000	Strong transcription	Brain Anterior Caudate	brain
14	chr7:56121000-56131200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr7:56121000-56131200	Strong transcription	Brain Hippocampus Middle	brain
16	chr7:56121200-56126000	Strong transcription	Colon Smooth Muscle	Colon
17	chr7:56121200-56128600	Strong transcription	HSMMtube	muscle
18	chr7:56121200-56129400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:56121200-56129400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr7:56121200-56129400	Strong transcription	Osteobl	bone
21	chr7:56121200-56130400	Strong transcription	Liver	Liver
22	chr7:56121200-56130600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr7:56121200-56130800	Strong transcription	Brain Cingulate Gyrus	brain
24	chr7:56121200-56130800	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr7:56121200-56131200	Strong transcription	Brain Germinal Matrix	brain
26	chr7:56121200-56131200	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr7:56121200-56131400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr7:56121200-56131400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr7:56121400-56125400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:56121400-56126000	Strong transcription	Fetal Kidney	kidney
31	chr7:56121400-56128000	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr7:56121400-56128000	Strong transcription	HSMM	muscle
33	chr7:56121400-56128400	Strong transcription	NH-A	brain
34	chr7:56121400-56129000	Genic enhancers	HepG2	liver
35	chr7:56121400-56129400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr7:56121400-56129800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr7:56121400-56130600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr7:56121400-56130800	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr7:56121400-56130800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr7:56121400-56130800	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr7:56121400-56131000	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr7:56121400-56131000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:56121400-56131000	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr7:56121400-56131200	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr7:56121400-56131200	Strong transcription	Placenta	Placenta
46	chr7:56121400-56131200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr7:56121400-56131200	Genic enhancers	Dnd41	blood
48	chr7:56121400-56131400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr7:56121400-56131400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr7:56121600-56127400	Strong transcription	Fetal Intestine Large	intestine

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