Variant report

Variant	rs13241531
Chromosome Location	chr7:56116652-56116653
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	HEY1	chr7:56116508-56116981	HepG2	liver:	n/a	n/a
2	POLR2A	chr7:56116370-56117415	K562	blood:	n/a	n/a
3	EP300	chr7:56115676-56117465	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr7:56115799-56116755	SK-N-SH	brain:	n/a	n/a
5	NFIC	chr7:56115846-56117003	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr7:56116560-56116710	HBMEC	blood vessel:	n/a	n/a
7	RAD21	chr7:56116578-56116726	HepG2	liver:	n/a	n/a
8	RCOR1	chr7:56116545-56116725	K562	blood:	n/a	n/a
9	POLR2A	chr7:56116524-56116924	MCF10A-Er-Src	breast:	n/a	n/a
10	ZNF143	chr7:56116576-56116714	K562	blood:	n/a	n/a
11	ZNF384	chr7:56115955-56116776	K562	blood:	n/a	n/a
12	CTCF	chr7:56116600-56116750	GM12874	blood:	n/a	n/a
13	POLR2A	chr7:56116441-56116939	HepG2	liver:	n/a	n/a
14	SETDB1	chr7:56116344-56116800	U2OS	brain:	n/a	n/a
15	GATA3	chr7:56115877-56116660	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56113304..56117542-chr7:56117614..56120307,4	K562	blood:

Variant related genes	Relation type
CCT6A	TF binding region
ENSG00000146731	Chromatin interaction
ENSG00000146733	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10085802	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253539	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253680	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13223519	1.00[ASN][1000 genomes]
rs13229704	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13233834	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13234504	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238029	0.91[EUR][1000 genomes]
rs13240361	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13247558	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151447	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013197	0.81[ASN][1000 genomes]
rs2304375	0.85[ASN][1000 genomes]
rs2331184	1.00[ASN][1000 genomes]
rs33922584	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34023503	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34154824	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34319969	1.00[ASN][1000 genomes]
rs34334997	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34573211	0.87[EUR][1000 genomes]
rs34822782	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35007015	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35033933	0.91[EUR][1000 genomes]
rs35058595	1.00[ASN][1000 genomes]
rs35102507	0.91[EUR][1000 genomes]
rs35136814	0.92[ASN][1000 genomes]
rs35347055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35506072	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35515485	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35523043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35581685	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35818005	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35881493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36044787	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36049923	1.00[ASN][1000 genomes]
rs36148650	0.91[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]
rs71543775	0.92[ASN][1000 genomes]
rs71543776	0.89[ASN][1000 genomes]
rs71543777	0.92[ASN][1000 genomes]
rs71543786	0.91[EUR][1000 genomes]
rs73126344	1.00[ASN][1000 genomes]
rs816219	0.83[ASN][1000 genomes]
rs816242	0.96[ASN][1000 genomes]
rs816412	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816413	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816415	0.84[EUR][1000 genomes];1.00[ASN][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:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56102200-56117600	Weak transcription	Gastric	stomach
2	chr7:56102200-56117600	Weak transcription	Spleen	Spleen
3	chr7:56102200-56117800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:56102200-56118200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:56102400-56117600	Weak transcription	Brain Anterior Caudate	brain
6	chr7:56102400-56117600	Weak transcription	GM12878-XiMat	blood
7	chr7:56102400-56117800	Weak transcription	Adipose Nuclei	Adipose
8	chr7:56102400-56117800	Weak transcription	Brain Substantia Nigra	brain
9	chr7:56102400-56118000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:56102400-56118000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr7:56102400-56118000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr7:56102400-56118000	Weak transcription	Left Ventricle	heart
13	chr7:56102400-56118000	Weak transcription	HSMMtube	muscle
14	chr7:56102400-56118000	Weak transcription	NHLF	lung
15	chr7:56102400-56118200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr7:56102600-56116800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr7:56102600-56117000	Weak transcription	Fetal Brain Female	brain
18	chr7:56102600-56117600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr7:56102600-56117800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr7:56102600-56117800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr7:56102600-56117800	Weak transcription	Brain Hippocampus Middle	brain
22	chr7:56102600-56118000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr7:56102600-56118000	Weak transcription	Right Atrium	heart
24	chr7:56102800-56118000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr7:56102800-56118200	Weak transcription	Primary B cells from cord blood	blood
26	chr7:56102800-56118200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr7:56103000-56118200	Weak transcription	Thymus	Thymus
28	chr7:56107200-56117800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr7:56108000-56117600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr7:56108000-56117600	Weak transcription	Fetal Brain Male	brain
31	chr7:56108800-56117600	Weak transcription	Esophagus	oesophagus
32	chr7:56108800-56117600	Weak transcription	Lung	lung
33	chr7:56108800-56118600	Weak transcription	Aorta	Aorta
34	chr7:56109400-56117800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr7:56110200-56117800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr7:56110400-56117600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr7:56110400-56117800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr7:56110400-56117800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr7:56110400-56118000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:56110400-56118000	Weak transcription	Ovary	ovary
41	chr7:56110600-56117600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr7:56110600-56117800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr7:56110600-56117800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr7:56110600-56117800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr7:56110600-56117800	Weak transcription	Placenta	Placenta
46	chr7:56110600-56118000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr7:56110600-56118200	Weak transcription	Primary T cells from cord blood	blood
48	chr7:56110800-56117200	Weak transcription	Dnd41	blood
49	chr7:56110800-56117600	Weak transcription	Hela-S3	cervix
50	chr7:56111000-56117800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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