Variant report

Variant	rs13229704
Chromosome Location	chr7:56122902-56122903
allele	C/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	chr7:56117687-56123706	K562	blood:	n/a	n/a
2	POLR2A	chr7:56122804-56123324	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:56120765-56123238	K562	blood:	n/a	n/a
4	POLR2A	chr7:56122844-56123466	HepG2	liver:	n/a	n/a
5	POLR2A	chr7:56122757-56123508	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr7:56122706-56123543	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr7:56122756-56124101	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr7:56122809-56123473	GM12892	blood:	n/a	n/a
9	POLR2A	chr7:56122839-56123637	HepG2	liver:	n/a	n/a
10	POLR2A	chr7:56122899-56123338	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56117123..56123487-chr7:56128716..56133468,11	MCF-7	breast:

Variant related genes	Relation type
PSPH	TF binding region
CCT6A	TF binding region
ENSG00000206603	TF binding region
ENSG00000146731	Chromatin interaction
ENSG00000129103	Chromatin interaction

Extended variants
information (count: 65 )
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	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12555	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13223519	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13232704	0.80[EUR][1000 genomes]
rs13233037	0.80[EUR][1000 genomes]
rs13233834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13234504	1.00[AFR][1000 genomes];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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13241531	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13247558	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151447	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013197	0.81[ASN][1000 genomes]
rs2304375	0.85[ASN][1000 genomes]
rs2331184	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33922584	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34023503	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34154824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34319969	1.00[ASN][1000 genomes]
rs34334997	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34573211	0.96[EUR][1000 genomes]
rs34822782	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35007015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35033933	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35058595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35102507	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35136814	0.92[ASN][1000 genomes]
rs35347055	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35506072	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35515485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35523043	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35581685	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35818005	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35881493	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36044787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36049923	1.00[ASN][1000 genomes]
rs36148650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778868	0.89[AMR][1000 genomes];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[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73126344	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs816219	0.83[ASN][1000 genomes]
rs816242	0.96[ASN][1000 genomes]
rs816412	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816413	1.00[AFR][1000 genomes];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: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	chr7:56120200-56124000	Weak transcription	Spleen	Spleen
2	chr7:56120200-56125600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:56120200-56131200	Weak transcription	Aorta	Aorta
4	chr7:56120400-56123000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:56120400-56123000	Weak transcription	Ovary	ovary
6	chr7:56120400-56124000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:56120400-56124000	Weak transcription	Gastric	stomach
8	chr7:56120600-56123600	Transcr. at gene 5' and 3'	A549	lung
9	chr7:56120600-56131000	Strong transcription	Adipose Nuclei	Adipose
10	chr7:56120800-56123000	Weak transcription	Right Ventricle	heart
11	chr7:56120800-56123200	Weak transcription	Psoas Muscle	Psoas
12	chr7:56120800-56123600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:56120800-56123800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
14	chr7:56120800-56123800	Weak transcription	Small Intestine	intestine
15	chr7:56120800-56124000	Weak transcription	Esophagus	oesophagus
16	chr7:56120800-56125200	Weak transcription	Colonic Mucosa	Colon
17	chr7:56120800-56127400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:56120800-56130000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr7:56120800-56130400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
20	chr7:56120800-56130800	Strong transcription	Brain Angular Gyrus	brain
21	chr7:56120800-56131200	Strong transcription	Fetal Thymus	thymus
22	chr7:56120800-56131400	Strong transcription	Fetal Muscle Leg	muscle
23	chr7:56120800-56131600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:56121000-56123000	Weak transcription	Primary B cells from cord blood	blood
25	chr7:56121000-56124200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
26	chr7:56121000-56124800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr7:56121000-56130000	Weak transcription	Stomach Mucosa	stomach
28	chr7:56121000-56130800	Strong transcription	Fetal Lung	lung
29	chr7:56121000-56131000	Strong transcription	Brain Anterior Caudate	brain
30	chr7:56121000-56131200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr7:56121000-56131200	Strong transcription	Brain Hippocampus Middle	brain
32	chr7:56121200-56123000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr7:56121200-56123000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr7:56121200-56123000	Weak transcription	Thymus	Thymus
35	chr7:56121200-56123200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr7:56121200-56124000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr7:56121200-56126000	Strong transcription	Colon Smooth Muscle	Colon
38	chr7:56121200-56128600	Strong transcription	HSMMtube	muscle
39	chr7:56121200-56129400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr7:56121200-56129400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr7:56121200-56129400	Strong transcription	Osteobl	bone
42	chr7:56121200-56130400	Strong transcription	Liver	Liver
43	chr7:56121200-56130600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr7:56121200-56130800	Strong transcription	Brain Cingulate Gyrus	brain
45	chr7:56121200-56130800	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr7:56121200-56131200	Strong transcription	Brain Germinal Matrix	brain
47	chr7:56121200-56131200	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:56121200-56131400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr7:56121200-56131400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr7:56121400-56123200	Weak transcription	Fetal Brain Male	brain

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