Variant report

Variant	rs12702519
Chromosome Location	chr7:6544247-6544248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:6530503..6532685-chr7:6541822..6544289,2	MCF-7	breast:
2	chr7:6414882..6417650-chr7:6542443..6546000,3	MCF-7	breast:
3	chr7:6521451..6526537-chr7:6541616..6547791,14	MCF-7	breast:
4	chr17:55528969..55531188-chr7:6542980..6544894,2	MCF-7	breast:
5	chr7:6527568..6529479-chr7:6542425..6544621,2	MCF-7	breast:
6	chr7:6542151..6545329-chr7:6615241..6617265,3	K562	blood:
7	chr7:6522337..6524449-chr7:6542969..6544719,2	K562	blood:
8	chr7:6530076..6532868-chr7:6542072..6546078,3	K562	blood:
9	chr7:6519406..6527633-chr7:6541095..6545327,10	MCF-7	breast:
10	chr7:6541964..6545996-chr7:6546800..6549452,3	K562	blood:
11	chr7:6543086..6544609-chr7:6628754..6631098,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231359	Chromatin interaction
ENSG00000146576	Chromatin interaction
ENSG00000136240	Chromatin interaction
ENSG00000136247	Chromatin interaction
ENSG00000269781	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10951986	0.82[ASW][hapmap];0.87[CHB][hapmap];0.89[LWK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs12702517	0.81[ASN][1000 genomes]
rs13233173	0.82[ASW][hapmap];0.87[CHB][hapmap];0.89[LWK][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs1523609	0.82[CHB][hapmap]
rs4720677	0.84[AFR][1000 genomes]
rs4724811	0.86[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4724812	0.81[ASN][1000 genomes]
rs6463564	0.86[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6463567	0.85[CHB][hapmap]
rs6463568	0.83[AFR][1000 genomes]
rs6959768	0.87[CHB][hapmap]
rs6964421	0.82[CHB][hapmap]
rs7778023	0.83[ASN][1000 genomes]
rs7788091	0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs7796667	0.81[ASN][1000 genomes]
rs7799479	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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
13	nsv887429	chr7:6520676-6659509	Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
14	nsv887430	chr7:6520676-6668027	Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
15	nsv508444	chr7:6534110-6700527	Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
16	nsv1025220	chr7:6534278-6736802	Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
17	nsv538717	chr7:6534278-6736802	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
18	nsv887431	chr7:6535517-6690240	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
19	nsv515978	chr7:6535517-6698905	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
20	nsv887432	chr7:6535517-6713985	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
21	esv3424341	chr7:6541877-6545575	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12702519	USP42	cis	cerebellar cortex	BrainEAC

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6540400-6545400	Weak transcription	Fetal Heart	heart
2	chr7:6542400-6544400	Active TSS	Fetal Intestine Large	intestine
3	chr7:6542400-6544400	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr7:6542400-6544600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr7:6542400-6544600	Active TSS	Lung	lung
6	chr7:6542600-6544400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr7:6542600-6544800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr7:6542600-6545000	Active TSS	Rectal Smooth Muscle	rectum
9	chr7:6542800-6544400	Active TSS	Esophagus	oesophagus
10	chr7:6542800-6544400	Active TSS	Pancreas	Pancrea
11	chr7:6542800-6544400	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr7:6542800-6544400	Bivalent/Poised TSS	HepG2	liver
13	chr7:6542800-6544600	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr7:6542800-6544600	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr7:6542800-6544600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:6542800-6544800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:6542800-6544800	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr7:6542800-6544800	Bivalent/Poised TSS	Fetal Brain Female	brain
19	chr7:6542800-6545000	Active TSS	H1 Cell Line	embryonic stem cell
20	chr7:6542800-6545000	Active TSS	Fetal Intestine Small	intestine
21	chr7:6543000-6544400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:6543000-6544400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:6543000-6544400	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr7:6543000-6544400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:6543000-6544400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:6543000-6544400	Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr7:6543000-6544400	Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr7:6543000-6544400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr7:6543000-6544400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr7:6543000-6544400	Active TSS	Brain Substantia Nigra	brain
31	chr7:6543000-6544400	Active TSS	Ovary	ovary
32	chr7:6543000-6544400	Active TSS	K562	blood
33	chr7:6543000-6544600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr7:6543000-6544600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:6543000-6544600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:6543000-6544600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr7:6543000-6544600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:6543000-6544600	Active TSS	Colon Smooth Muscle	Colon
39	chr7:6543000-6544600	Active TSS	Psoas Muscle	Psoas
40	chr7:6543000-6544600	Active TSS	Small Intestine	intestine
41	chr7:6543000-6544800	Active TSS	Brain Anterior Caudate	brain
42	chr7:6543000-6544800	Active TSS	Fetal Kidney	kidney
43	chr7:6543000-6545000	Active TSS	Primary T cells from cord blood	blood
44	chr7:6543200-6544400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr7:6543200-6544400	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr7:6543200-6544400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr7:6543200-6544400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr7:6543200-6544400	Active TSS	Brain Cingulate Gyrus	brain
49	chr7:6543200-6544400	Active TSS	Right Atrium	heart
50	chr7:6543200-6544400	Active TSS	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links