Variant report

Variant	rs13240753
Chromosome Location	chr7:6518398-6518399
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	chr7:6511092-6518405	IMR90	lung:	n/a	n/a
2	POLR2A	chr7:6517553-6518957	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:6511024-6519040	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6517704..6522059-chr7:6522068..6526480,12	K562	blood:
2	chr7:6515936..6521284-chr7:6521487..6524392,7	MCF-7	breast:
3	chr7:6510413..6513811-chr7:6516009..6519454,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269781	TF binding region
ENSG00000136240	Chromatin interaction
ENSG00000269781	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10951985	0.82[ASN][1000 genomes]
rs11761728	0.98[ASN][1000 genomes]
rs11768661	0.98[ASN][1000 genomes]
rs12112241	0.98[ASN][1000 genomes]
rs12702511	0.95[ASN][1000 genomes]
rs12702512	0.95[ASN][1000 genomes]
rs12702514	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13222291	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17136294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2246223	0.84[ASW][hapmap]
rs4574760	0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4720675	0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs55707863	0.87[ASN][1000 genomes]
rs62454714	0.98[ASN][1000 genomes]
rs6974535	0.98[ASN][1000 genomes]
rs836504	1.00[LWK][hapmap]
rs9801058	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
3	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
5	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
6	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
7	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv497874	chr7:6296768-6614902	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	esv1824738	chr7:6431933-6554222	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	esv1825865	chr7:6431933-6554222	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv1026878	chr7:6490387-6592374	Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
12	nsv830895	chr7:6514781-6722092	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13240753	RNF216L	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6499600-6521800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:6503600-6522800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:6505000-6521400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr7:6507000-6519400	Weak transcription	Fetal Heart	heart
5	chr7:6507600-6522400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:6507800-6522600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:6508000-6520200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:6508000-6522000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:6509200-6521400	Strong transcription	NHEK	skin
10	chr7:6509800-6519600	Weak transcription	Fetal Kidney	kidney
11	chr7:6509800-6522000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:6510200-6518800	Weak transcription	Small Intestine	intestine
13	chr7:6510200-6519600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr7:6510200-6522200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr7:6510200-6522400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:6510200-6522600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr7:6510400-6519800	Weak transcription	Brain Anterior Caudate	brain
18	chr7:6511600-6521600	Weak transcription	Fetal Brain Male	brain
19	chr7:6512200-6520800	Weak transcription	Esophagus	oesophagus
20	chr7:6512800-6519400	Weak transcription	Brain Germinal Matrix	brain
21	chr7:6513200-6518800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr7:6513200-6518800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr7:6513200-6519800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr7:6513200-6522400	Weak transcription	Aorta	Aorta
25	chr7:6513200-6522400	Weak transcription	Lung	lung
26	chr7:6513400-6518800	Weak transcription	Fetal Brain Female	brain
27	chr7:6513400-6521200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr7:6513400-6521200	Weak transcription	Brain Substantia Nigra	brain
29	chr7:6513600-6521200	Weak transcription	Fetal Lung	lung
30	chr7:6513800-6520000	Weak transcription	Colonic Mucosa	Colon
31	chr7:6513800-6520600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr7:6514000-6519600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr7:6514000-6519600	Weak transcription	Brain Hippocampus Middle	brain
34	chr7:6514000-6522400	Weak transcription	Thymus	Thymus
35	chr7:6514200-6518400	Genic enhancers	HepG2	liver
36	chr7:6514200-6519400	Weak transcription	Hela-S3	cervix
37	chr7:6514200-6520000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr7:6514200-6522000	Genic enhancers	Fetal Muscle Leg	muscle
39	chr7:6514400-6519600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr7:6514600-6519600	Weak transcription	A549	lung
41	chr7:6514600-6519800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:6514800-6519400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr7:6514800-6521400	Weak transcription	HMEC	breast
44	chr7:6515000-6519400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr7:6515000-6519800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr7:6515400-6519400	Weak transcription	Spleen	Spleen
47	chr7:6515400-6519400	Weak transcription	NHLF	lung
48	chr7:6515400-6519600	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr7:6515400-6519600	Weak transcription	HUVEC	blood vessel
50	chr7:6516000-6519600	Weak transcription	Primary T cells from cord blood	blood

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