Variant report

Variant	rs9845460
Chromosome Location	chr3:136587117-136587118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136581625..136583340-chr3:136586499..136589172,2	K562	blood:
2	chr3:136580996..136583825-chr3:136586940..136590069,3	MCF-7	breast:
3	chr3:136580474..136583340-chr3:136584375..136587999,4	K562	blood:

Variant related genes	Relation type
ENSG00000239213	Chromatin interaction
ENSG00000158092	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10470440	0.81[MKK][hapmap]
rs1052618	0.91[LWK][hapmap];0.81[MKK][hapmap]
rs10804645	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs108858	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs11711599	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11717974	0.92[ASN][1000 genomes]
rs12054220	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12629000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12630955	0.80[AFR][1000 genomes]
rs13077864	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095028	0.90[CHD][hapmap]
rs1406539	1.00[ASW][hapmap];0.95[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1569228	0.91[LWK][hapmap]
rs16844241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171519	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1965107	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2043365	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2176270	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361232	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs361233	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs361235	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs361238	1.00[CHB][hapmap]
rs361240	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs361253	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4678271	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4678275	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];0.94[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4678447	1.00[ASW][hapmap];0.95[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410363	0.96[ASN][1000 genomes]
rs62410438	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71630059	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610507	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7631541	1.00[ASW][hapmap];0.95[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648198	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7648817	0.93[LWK][hapmap]
rs835636	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs835637	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs835652	0.86[CHB][hapmap]
rs9682783	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9818397	0.93[LWK][hapmap]
rs9819572	0.93[LWK][hapmap]
rs9828009	0.93[LWK][hapmap];0.81[MKK][hapmap]
rs9845076	0.86[CHB][hapmap];1.00[CHD][hapmap]

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	nsv877530	chr3:136514310-136604697	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
2	nsv877531	chr3:136517016-136662954	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv877532	chr3:136526939-136662603	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv877533	chr3:136539689-136662954	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9845460	MSL2	cis	cerebellum	SCAN
rs9845460	TMEM22	cis	cerebellum	SCAN
rs9845460	NCK1	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136582000-136587800	Weak transcription	Lung	lung
2	chr3:136582000-136591400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:136582000-136591400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:136582000-136592600	Weak transcription	Gastric	stomach
5	chr3:136582000-136601400	Weak transcription	Spleen	Spleen
6	chr3:136582200-136591400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:136582200-136591400	Weak transcription	Left Ventricle	heart
8	chr3:136582200-136594000	Weak transcription	Esophagus	oesophagus
9	chr3:136582400-136587800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:136582400-136590800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:136582400-136590800	Weak transcription	Right Atrium	heart
12	chr3:136582400-136591400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:136582400-136593000	Weak transcription	Right Ventricle	heart
14	chr3:136582400-136594600	Weak transcription	Colonic Mucosa	Colon
15	chr3:136582400-136602600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:136582400-136612600	Weak transcription	Pancreas	Pancrea
17	chr3:136582600-136587200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:136582600-136587400	Weak transcription	Fetal Intestine Small	intestine
19	chr3:136582600-136587400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:136582600-136587600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:136582600-136587600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:136582600-136587800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:136582600-136588000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:136582600-136589400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:136582600-136590000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr3:136582600-136590000	Weak transcription	NHDF-Ad	bronchial
27	chr3:136582600-136590400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:136582600-136590400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr3:136582600-136590400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:136582600-136591400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:136582600-136591400	Weak transcription	Aorta	Aorta
32	chr3:136582600-136591400	Weak transcription	A549	lung
33	chr3:136582600-136592200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:136582600-136592400	Weak transcription	Fetal Lung	lung
35	chr3:136582600-136592600	Weak transcription	HUVEC	blood vessel
36	chr3:136582600-136593200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr3:136582600-136593800	Weak transcription	Brain Substantia Nigra	brain
38	chr3:136582600-136595000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:136582600-136595600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr3:136582600-136601400	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:136582600-136602000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:136582600-136604200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:136582600-136604200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:136582600-136612600	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:136582600-136612600	Weak transcription	NH-A	brain
46	chr3:136582600-136612600	Weak transcription	Osteobl	bone
47	chr3:136582800-136587800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:136582800-136588000	Weak transcription	Placenta	Placenta
49	chr3:136582800-136589600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:136582800-136590400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links