Variant report

Variant	rs12610606
Chromosome Location	chr19:38765822-38765823
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38763683..38766666-chr19:38812361..38813866,2	K562	blood:
2	chr19:38765291..38770264-chr19:38793708..38796948,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167644	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12610791	0.81[CHB][hapmap]
rs12983492	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs2060244	0.97[ASN][1000 genomes]
rs34276782	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34508901	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35029752	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35366094	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3745949	0.97[ASN][1000 genomes]
rs3786874	0.88[ASW][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap]
rs6508781	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71354994	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7245454	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7253823	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7254637	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7259936	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73037326	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12610606	RPS16	cis	parietal	SCAN
rs12610606	CEACAM5	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38756600-38772600	Weak transcription	Primary T cells from cord blood	blood
2	chr19:38756600-38772600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:38756800-38772600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr19:38756800-38774800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr19:38756800-38775000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:38756800-38778600	Weak transcription	Thymus	Thymus
7	chr19:38756800-38779600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr19:38758000-38770800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:38758000-38770800	Weak transcription	Primary B cells from cord blood	blood
10	chr19:38758000-38774200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr19:38758200-38770800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:38758400-38774400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr19:38758800-38770600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr19:38759000-38768000	Weak transcription	Esophagus	oesophagus
15	chr19:38759000-38770800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr19:38759400-38770800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr19:38759600-38783200	Weak transcription	Fetal Brain Male	brain
18	chr19:38759800-38768200	Weak transcription	Fetal Kidney	kidney
19	chr19:38760800-38766000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr19:38761200-38769000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr19:38761400-38770600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:38761600-38766800	Weak transcription	NHLF	lung
23	chr19:38761600-38767400	Strong transcription	NHEK	skin
24	chr19:38761600-38767800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr19:38761600-38767800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:38761600-38767800	Weak transcription	HSMM	muscle
27	chr19:38761600-38767800	Weak transcription	HSMMtube	muscle
28	chr19:38761600-38768200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr19:38761600-38768800	Weak transcription	Fetal Thymus	thymus
30	chr19:38761600-38769000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr19:38761600-38770800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:38761600-38770800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr19:38761600-38773000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr19:38761800-38767400	Weak transcription	NHDF-Ad	bronchial
35	chr19:38761800-38767600	Weak transcription	Osteobl	bone
36	chr19:38761800-38767800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:38761800-38768400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr19:38761800-38770800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr19:38764200-38768600	Weak transcription	Fetal Stomach	stomach
40	chr19:38764400-38766200	Enhancers	Lung	lung
41	chr19:38764400-38767800	Weak transcription	Spleen	Spleen
42	chr19:38764400-38771200	Weak transcription	Liver	Liver
43	chr19:38764600-38768200	Weak transcription	HepG2	liver
44	chr19:38764800-38766200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr19:38764800-38768800	Enhancers	Fetal Heart	heart
46	chr19:38765000-38766400	Enhancers	Brain Cingulate Gyrus	brain
47	chr19:38765000-38767000	Enhancers	Aorta	Aorta
48	chr19:38765200-38766000	Enhancers	Brain Anterior Caudate	brain
49	chr19:38765200-38766000	Enhancers	Brain Substantia Nigra	brain
50	chr19:38765200-38766200	Enhancers	Brain Hippocampus Middle	brain

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