Variant report

Variant	rs7259936
Chromosome Location	chr19:38772978-38772979
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	chr19:38759485..38762494-chr19:38770790..38773902,4	K562	blood:
2	chr19:38759881..38761740-chr19:38772402..38774668,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12610606	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]
rs12610791	0.81[CHB][hapmap]
rs12983492	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs2060244	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34276782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34508901	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34992016	0.80[ASN][1000 genomes]
rs35029752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35366094	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3745949	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3786874	0.88[ASW][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs3786875	0.81[AFR][1000 genomes]
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];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71354994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7245454	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7253823	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7254637	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73037307	0.81[AFR][1000 genomes]
rs73037309	0.81[AFR][1000 genomes]
rs73037326	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7259936	SLC1A5	cis	parietal	SCAN
rs7259936	CEACAM5	cis	parietal	SCAN
rs7259936	RPS16	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38756800-38774800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr19:38756800-38775000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:38756800-38778600	Weak transcription	Thymus	Thymus
4	chr19:38756800-38779600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr19:38758000-38774200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr19:38758400-38774400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr19:38759600-38783200	Weak transcription	Fetal Brain Male	brain
8	chr19:38761600-38773000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:38765800-38794800	Weak transcription	Small Intestine	intestine
10	chr19:38769200-38773800	Weak transcription	Stomach Mucosa	stomach
11	chr19:38769200-38774400	Genic enhancers	HMEC	breast
12	chr19:38769200-38774800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:38769200-38778400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:38769200-38791200	Weak transcription	Fetal Kidney	kidney
15	chr19:38769400-38776000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr19:38769400-38779200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr19:38769400-38795200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr19:38769600-38775200	Weak transcription	NHDF-Ad	bronchial
19	chr19:38769600-38778400	Weak transcription	Brain Substantia Nigra	brain
20	chr19:38769800-38773000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr19:38769800-38775600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr19:38769800-38775800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr19:38769800-38778000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:38769800-38778200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:38769800-38778200	Weak transcription	Brain Hippocampus Middle	brain
26	chr19:38769800-38779000	Weak transcription	Brain Anterior Caudate	brain
27	chr19:38769800-38779000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr19:38769800-38779000	Weak transcription	HSMM	muscle
29	chr19:38769800-38779200	Weak transcription	Brain Angular Gyrus	brain
30	chr19:38769800-38780400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:38770000-38774000	Weak transcription	HUVEC	blood vessel
32	chr19:38770000-38780600	Weak transcription	Brain Germinal Matrix	brain
33	chr19:38770400-38773200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr19:38770400-38774200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:38770400-38774400	Genic enhancers	NHEK	skin
36	chr19:38770600-38777000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr19:38770800-38773200	Strong transcription	Primary B cells from cord blood	blood
38	chr19:38770800-38773400	Genic enhancers	A549	lung
39	chr19:38770800-38775000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr19:38770800-38785800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:38771200-38774000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:38771200-38774000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr19:38771200-38776000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr19:38771200-38779000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr19:38771400-38773000	Weak transcription	Left Ventricle	heart
46	chr19:38771400-38773200	Weak transcription	Colonic Mucosa	Colon
47	chr19:38771400-38773200	Weak transcription	Fetal Intestine Large	intestine
48	chr19:38771400-38773800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr19:38771400-38774000	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr19:38771400-38774800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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