Variant report

Variant	rs4930712
Chromosome Location	chr12:124080682-124080683
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123848402..123850885-chr12:124079862..124083002,3	MCF-7	breast:
2	chr12:124080644..124082674-chr12:124097166..124099326,2	K562	blood:
3	chr12:123755326..123757299-chr12:124079928..124082713,2	MCF-7	breast:
4	chr12:124075051..124078239-chr12:124079848..124084285,5	K562	blood:
5	chr12:124069965..124078255-chr12:124078837..124084347,12	K562	blood:
6	chr12:124076446..124078757-chr12:124080091..124082095,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000086598	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000111364	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1050443	0.92[EUR][1000 genomes]
rs1050448	0.84[EUR][1000 genomes]
rs1050449	0.84[EUR][1000 genomes]
rs1056132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057301	0.83[EUR][1000 genomes]
rs11833889	0.88[EUR][1000 genomes]
rs12809853	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816883	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12829500	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15587	0.88[EUR][1000 genomes]
rs16917551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3190835	0.85[EUR][1000 genomes]
rs3204541	0.88[EUR][1000 genomes]
rs34097324	0.88[EUR][1000 genomes]
rs34369761	0.82[EUR][1000 genomes]
rs34514002	0.87[EUR][1000 genomes]
rs35064645	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35708602	0.88[EUR][1000 genomes]
rs35867744	0.88[EUR][1000 genomes]
rs36002329	0.99[EUR][1000 genomes]
rs3850952	0.81[EUR][1000 genomes]
rs4930704	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4930709	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930713	0.83[EUR][1000 genomes]
rs4930714	0.83[EUR][1000 genomes]
rs55705511	0.85[EUR][1000 genomes]
rs56213464	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56675602	0.88[EUR][1000 genomes]
rs59126974	0.87[EUR][1000 genomes]
rs6488877	0.86[ASN][1000 genomes]
rs6488884	0.84[EUR][1000 genomes]
rs66494087	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66694750	0.88[EUR][1000 genomes]
rs68163141	0.86[EUR][1000 genomes]
rs7137473	0.87[EUR][1000 genomes]
rs7139162	0.87[EUR][1000 genomes]
rs71458807	0.93[EUR][1000 genomes]
rs71458808	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308304	0.88[EUR][1000 genomes]
rs7309292	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313207	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313751	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7398935	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7953876	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956299	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7962151	0.86[ASN][1000 genomes]
rs7963804	0.86[ASN][1000 genomes]
rs7972380	0.83[EUR][1000 genomes]
rs7973766	0.82[EUR][1000 genomes]
rs7979561	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS 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 miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4930712	TCTN2	cis	Adipose Subcutaneous	GTEx
rs4930712	TCTN2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124070000-124085800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:124070600-124082200	Strong transcription	Fetal Muscle Leg	muscle
3	chr12:124070600-124084400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:124071200-124082800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:124071200-124083400	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:124071200-124083400	Strong transcription	Fetal Intestine Large	intestine
7	chr12:124071200-124083600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:124071200-124083600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr12:124071200-124083600	Strong transcription	Fetal Muscle Trunk	muscle
10	chr12:124071200-124083800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:124071200-124083800	Strong transcription	Placenta	Placenta
12	chr12:124071200-124084000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:124071200-124084000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr12:124071200-124084800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:124071400-124082800	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr12:124071400-124083000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:124071600-124084400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr12:124071800-124083600	Strong transcription	Primary hematopoietic stem cells	blood
19	chr12:124072200-124085800	Weak transcription	Small Intestine	intestine
20	chr12:124072400-124082200	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr12:124072400-124083800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:124072600-124082400	Strong transcription	Thymus	Thymus
23	chr12:124072600-124083400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:124072600-124083400	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:124072800-124084200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:124073000-124083600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:124073200-124084200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:124073400-124082400	Strong transcription	NHEK	skin
29	chr12:124073400-124084000	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:124073600-124081600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr12:124073600-124081800	Strong transcription	Colonic Mucosa	Colon
32	chr12:124073600-124082400	Strong transcription	Fetal Brain Female	brain
33	chr12:124073600-124083400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr12:124073600-124083600	Strong transcription	Primary B cells from peripheral blood	blood
35	chr12:124073600-124083800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:124073600-124083800	Strong transcription	Left Ventricle	heart
37	chr12:124073800-124082200	Strong transcription	Brain Angular Gyrus	brain
38	chr12:124073800-124082200	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr12:124073800-124083000	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr12:124073800-124083200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:124073800-124083400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr12:124073800-124083600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr12:124073800-124083800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:124073800-124083800	Strong transcription	Stomach Smooth Muscle	stomach
45	chr12:124073800-124084200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:124073800-124084600	Strong transcription	Fetal Thymus	thymus
47	chr12:124073800-124085200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:124073800-124085400	Weak transcription	Stomach Mucosa	stomach
49	chr12:124074000-124083200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr12:124074000-124083800	Strong transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links