Variant report

Variant	rs15587
Chromosome Location	chr12:124104049-124104050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124102971..124106526-chr12:124116602..124119947,4	MCF-7	breast:
2	chr12:124102693..124104593-chr12:124116530..124119850,3	K562	blood:
3	chr12:124098960..124101671-chr12:124104037..124106879,4	MCF-7	breast:
4	chr12:124088181..124092597-chr12:124103308..124106149,5	K562	blood:
5	chr12:124103214..124105859-chr12:124106055..124109639,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111361	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000206897	Chromatin interaction
ENSG00000111364	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1022320	1.00[CHB][hapmap]
rs1022321	1.00[CHB][hapmap]
rs1050443	0.92[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1050448	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1050449	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056132	0.88[EUR][1000 genomes]
rs10744162	1.00[JPT][hapmap]
rs10773034	1.00[JPT][hapmap]
rs10846559	1.00[CHB][hapmap]
rs11057355	1.00[CHB][hapmap]
rs1114628	1.00[CHB][hapmap]
rs11612927	1.00[JPT][hapmap]
rs11833889	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835252	1.00[CHB][hapmap]
rs12809853	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs12816883	0.83[EUR][1000 genomes]
rs12829500	0.91[EUR][1000 genomes]
rs1568030	1.00[CHB][hapmap]
rs16917551	0.88[EUR][1000 genomes]
rs2340692	1.00[CHB][hapmap]
rs3190835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3204541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34097324	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34514002	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35016092	0.89[ASN][1000 genomes]
rs35064645	0.88[EUR][1000 genomes]
rs35708602	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35867744	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36002329	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850952	0.92[CEU][hapmap]
rs4930709	0.90[EUR][1000 genomes]
rs4930712	0.88[EUR][1000 genomes]
rs4930713	0.92[CEU][hapmap]
rs4930714	0.92[CEU][hapmap]
rs4930737	1.00[JPT][hapmap]
rs55705511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56213464	0.91[EUR][1000 genomes]
rs56675602	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59126974	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488878	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6488884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66494087	0.87[EUR][1000 genomes]
rs66694750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68163141	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137473	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139162	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71458807	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71458808	0.91[EUR][1000 genomes]
rs7308304	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309292	0.88[EUR][1000 genomes]
rs7313207	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs7953876	0.87[EUR][1000 genomes]
rs7959714	0.89[ASN][1000 genomes]
rs7974279	1.00[JPT][hapmap]
rs7979561	0.89[EUR][1000 genomes]
rs9919	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1040356	chr12:124094758-124172731	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs15587	TCTN2	cis	Artery Tibial	GTEx
rs15587	TCTN2	cis	Adipose Subcutaneous	GTEx
rs15587	EIF2B1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124087800-124109600	Weak transcription	Right Atrium	heart
2	chr12:124088000-124107200	Strong transcription	K562	blood
3	chr12:124088200-124116000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:124088200-124117000	Strong transcription	Fetal Stomach	stomach
5	chr12:124088400-124105800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:124088400-124108000	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr12:124088400-124116000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:124088400-124116000	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:124088400-124116000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:124088400-124116000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:124088400-124116000	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:124088400-124116200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:124088400-124116800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr12:124088400-124117000	Strong transcription	Fetal Intestine Small	intestine
15	chr12:124088600-124104800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:124088600-124107400	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr12:124088600-124116000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:124088600-124116000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:124088600-124116000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr12:124088600-124116000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:124088600-124116000	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:124088600-124116000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr12:124088600-124116200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr12:124088600-124116200	Strong transcription	Fetal Thymus	thymus
25	chr12:124088600-124116800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:124088600-124116800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:124088600-124116800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr12:124088600-124117000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr12:124088800-124107600	Strong transcription	NH-A	brain
30	chr12:124088800-124116000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:124088800-124116000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:124088800-124116000	Strong transcription	Fetal Intestine Large	intestine
33	chr12:124089000-124105800	Strong transcription	Fetal Muscle Leg	muscle
34	chr12:124089000-124107400	Strong transcription	Fetal Lung	lung
35	chr12:124089000-124116000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:124089000-124116200	Strong transcription	Brain Germinal Matrix	brain
37	chr12:124089200-124107400	Strong transcription	Hela-S3	cervix
38	chr12:124089200-124115400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr12:124089200-124116000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:124089200-124116000	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr12:124089200-124116000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:124089200-124116200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:124089200-124116400	Strong transcription	Liver	Liver
44	chr12:124089200-124116600	Strong transcription	Stomach Smooth Muscle	stomach
45	chr12:124089600-124116000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:124089600-124116000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr12:124089600-124116000	Strong transcription	Duodenum Mucosa	Duodenum
48	chr12:124089800-124107000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:124089800-124116200	Strong transcription	Thymus	Thymus
50	chr12:124089800-124117000	Strong transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links