Variant report

Variant	rs16846526
Chromosome Location	chr1:173856237-173856238
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173853137..173856860-chr1:173858771..173862944,6	K562	blood:
2	chr1:173828135..173830893-chr1:173854579..173857617,3	MCF-7	breast:
3	chr1:173844210..173845835-chr1:173854372..173856264,2	K562	blood:
4	chr1:173854070..173860394-chr1:173860539..173867294,11	MCF-7	breast:
5	chr1:173846519..173848923-chr1:173855106..173856720,2	K562	blood:
6	chr1:173856030..173858273-chr1:173864244..173866649,2	K562	blood:
7	chr1:173855077..173857182-chr1:173858771..173861573,3	K562	blood:
8	chr1:173831191..173840458-chr1:173852193..173864862,18	MCF-7	breast:
9	chr1:173845188..173847906-chr1:173855416..173857290,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185278	Chromatin interaction
ENSG00000270084	Chromatin interaction
ENSG00000208317	Chromatin interaction
ENSG00000234741	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs16846418	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16846433	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846478	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846593	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2065170	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068871	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2146372	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2227592	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2235095	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2759328	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791021	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3791022	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs57022387	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58994962	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59393482	0.83[AMR][1000 genomes]
rs60689957	0.83[AMR][1000 genomes]
rs61262741	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61649485	0.84[ASN][1000 genomes]
rs6656255	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6685043	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6691053	0.82[CHB][hapmap]
rs6696381	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6790	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7521960	0.83[AFR][1000 genomes]
rs941987	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs941988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9970048	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs16846526	SNORD78	cis	parietal	SCAN
rs16846526	dJ383J4.3	cis	multi-tissue	Pritchard
rs16846526		cis	Lymphoblastoid	GTEx
rs16846526	CENPL	cis	lymphoblastoid	seeQTL
rs16846526	SNORD79	cis	parietal	SCAN
rs16846526	SNORD80	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173838200-173866000	Weak transcription	Small Intestine	intestine
2	chr1:173838400-173860200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:173839000-173862800	Weak transcription	HMEC	breast
4	chr1:173840200-173856800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:173841000-173864400	Weak transcription	Fetal Heart	heart
6	chr1:173841000-173868600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:173842800-173859200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:173853200-173858000	Strong transcription	Fetal Muscle Leg	muscle
9	chr1:173853400-173856400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:173853400-173857800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:173853400-173865200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:173853800-173858600	Strong transcription	Placenta	Placenta
13	chr1:173854000-173857400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:173854000-173858800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:173854000-173858800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr1:173854000-173859400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:173854200-173856800	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:173854200-173857000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:173854200-173857000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:173854200-173857200	Strong transcription	Brain Anterior Caudate	brain
21	chr1:173854200-173857600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr1:173854200-173858200	Strong transcription	Left Ventricle	heart
23	chr1:173854200-173858800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:173854400-173856400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:173854600-173856600	Strong transcription	Brain Germinal Matrix	brain
26	chr1:173854600-173857000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:173854600-173857400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:173854600-173857600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:173854600-173858400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr1:173854600-173858600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:173854800-173856400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:173854800-173856400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:173854800-173856400	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr1:173854800-173856400	Strong transcription	Fetal Lung	lung
35	chr1:173854800-173856400	Strong transcription	Rectal Smooth Muscle	rectum
36	chr1:173854800-173856400	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:173854800-173856600	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:173854800-173857000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:173854800-173857200	Strong transcription	Adipose Nuclei	Adipose
40	chr1:173854800-173857400	Strong transcription	Brain Cingulate Gyrus	brain
41	chr1:173854800-173857400	Strong transcription	Brain Hippocampus Middle	brain
42	chr1:173854800-173857400	Strong transcription	HepG2	liver
43	chr1:173854800-173857400	Strong transcription	HSMM	muscle
44	chr1:173854800-173857600	Strong transcription	Primary hematopoietic stem cells	blood
45	chr1:173854800-173857600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
46	chr1:173854800-173857800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr1:173854800-173858600	Strong transcription	Liver	Liver
48	chr1:173855000-173856600	Strong transcription	NHDF-Ad	bronchial
49	chr1:173855000-173857400	Strong transcription	Fetal Intestine Large	intestine
50	chr1:173855000-173857600	Strong transcription	Fetal Kidney	kidney

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