Variant report

Variant	rs9870858
Chromosome Location	chr3:49769071-49769072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49761055..49763701-chr3:49764283..49769369,4	MCF-7	breast:
2	chr3:49765843..49767368-chr3:49767924..49770492,2	K562	blood:
3	chr3:49719733..49721602-chr3:49767313..49769950,2	K562	blood:
4	chr3:49763618..49765527-chr3:49766623..49769354,2	K562	blood:

Variant related genes	Relation type
ENSG00000164062	Chromatin interaction
ENSG00000173540	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10452032	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1078341	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10865956	1.00[CHD][hapmap]
rs11130208	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11130211	0.94[CEU][hapmap]
rs11130217	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709734	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11720705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12583	1.00[CHD][hapmap]
rs12637313	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap]
rs12715437	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13091525	1.00[ASN][1000 genomes]
rs1352889	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1491983	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs1491985	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1532204	0.94[CEU][hapmap]
rs1586827	1.00[CEU][hapmap]
rs1799844	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982861	1.00[CHD][hapmap]
rs1996663	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1996664	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2029591	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs2131108	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2312462	1.00[CHD][hapmap]
rs2329021	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs28535523	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3020779	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs34890793	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs35012435	1.00[ASN][1000 genomes]
rs35129566	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35491931	1.00[ASN][1000 genomes]
rs4241405	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs4241407	1.00[CHD][hapmap]
rs4855833	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4855845	1.00[CEU][hapmap]
rs4855846	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4855882	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4855885	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs55997059	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58339610	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59357103	0.92[EUR][1000 genomes]
rs59684465	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61557789	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62260663	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260720	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260723	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62260755	1.00[ASN][1000 genomes]
rs62262061	1.00[ASN][1000 genomes]
rs62262106	1.00[ASN][1000 genomes]
rs62262118	1.00[ASN][1000 genomes]
rs62262722	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262730	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446285	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs6774202	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6787892	1.00[ASN][1000 genomes]
rs6790568	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6797299	0.94[CEU][hapmap]
rs6804970	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809879	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71326904	1.00[ASN][1000 genomes]
rs7613603	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615318	1.00[ASN][1000 genomes]
rs7620848	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621797	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7635601	1.00[ASN][1000 genomes]
rs7637711	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649428	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824435	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs9829155	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830730	1.00[CEU][hapmap]
rs9835157	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836756	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849038	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs9851651	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862534	1.00[CHD][hapmap]
rs9870755	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883000	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv967216	chr3:49764885-49776535	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs9870858	AMT	cis	Thyroid	GTEx
rs9870858	RNF123	cis	Artery Tibial	GTEx
rs9870858	RBM6	cis	cerebellum	SCAN
rs9870858	ZNF589	cis	parietal	SCAN
rs9870858	AMT	cis	lung	GTEx
rs9870858	DALRD3	cis	cerebellum	SCAN
rs9870858	AMT	cis	parietal	SCAN
rs9870858	GNL3	cis	cerebellum	SCAN
rs9870858	ITIH3	cis	cerebellum	SCAN
rs9870858	OR9G4	trans	parietal	SCAN
rs9870858	DALRD3	cis	parietal	SCAN
rs9870858	RNF123	cis	parietal	SCAN
rs9870858	P4HTM	cis	parietal	SCAN
rs9870858	GMPPB	cis	parietal	SCAN
rs9870858	WDR6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49762000-49770000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:49762000-49773800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49762000-49775000	Weak transcription	Psoas Muscle	Psoas
4	chr3:49762000-49778000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:49762400-49771000	Strong transcription	Brain Inferior Temporal Lobe	brain
6	chr3:49762400-49772200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:49762400-49773000	Weak transcription	Fetal Heart	heart
8	chr3:49762400-49776800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:49762400-49781600	Strong transcription	Fetal Stomach	stomach
10	chr3:49762600-49770400	Strong transcription	Brain Germinal Matrix	brain
11	chr3:49762600-49774600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:49762600-49776400	Strong transcription	Fetal Brain Female	brain
13	chr3:49762600-49776800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:49762600-49777000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:49762600-49777200	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:49762600-49777600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:49762600-49781800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:49762600-49785200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:49762600-49809000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:49762800-49770000	Strong transcription	Fetal Intestine Small	intestine
21	chr3:49762800-49770800	Strong transcription	Fetal Intestine Large	intestine
22	chr3:49762800-49771000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr3:49762800-49775600	Strong transcription	Fetal Thymus	thymus
24	chr3:49762800-49776400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:49762800-49776600	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:49763000-49770800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:49763000-49776400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:49763000-49776600	Strong transcription	Placenta	Placenta
29	chr3:49763000-49776800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:49763000-49784800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:49763200-49770600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:49763200-49776400	Strong transcription	Dnd41	blood
33	chr3:49763400-49773600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:49764000-49776000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:49764000-49776400	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr3:49764000-49781800	Strong transcription	Fetal Muscle Leg	muscle
37	chr3:49764200-49776600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:49764200-49776600	Strong transcription	Primary T cells from cord blood	blood
39	chr3:49764600-49769800	Weak transcription	Small Intestine	intestine
40	chr3:49764800-49771600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:49764800-49776600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr3:49765800-49769400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:49765800-49769600	Weak transcription	Pancreas	Pancrea
44	chr3:49765800-49770000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr3:49765800-49770000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:49765800-49770000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:49765800-49770000	Weak transcription	Esophagus	oesophagus
48	chr3:49765800-49770800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:49765800-49772000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:49765800-49775200	Weak transcription	Stomach Mucosa	stomach

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