Variant report

Variant	rs6545040
Chromosome Location	chr2:48676931-48676932
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48668357..48671385-chr2:48673634..48677025,4	K562	blood:
2	chr2:48671387..48674060-chr2:48675787..48677578,2	K562	blood:
3	chr2:48676760..48679121-chr2:48771521..48774088,2	K562	blood:
4	chr2:48666517..48672497-chr2:48674609..48679967,9	MCF-7	breast:
5	chr2:48666372..48668105-chr2:48676694..48678547,2	MCF-7	breast:
6	chr2:48335435..48337113-chr2:48675018..48677889,2	K562	blood:
7	chr2:48010725..48012661-chr2:48674765..48677186,2	K562	blood:

Variant related genes	Relation type
ENSG00000162869	Chromatin interaction
ENSG00000272663	Chromatin interaction
ENSG00000116062	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10185212	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10865229	0.86[ASN][1000 genomes]
rs11677398	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12477901	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs13386132	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3811520	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4328683	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4371401	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4429520	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap]
rs4430989	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4464333	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952913	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4953574	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4953584	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4953585	1.00[EUR][1000 genomes]
rs4953588	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4953590	0.87[EUR][1000 genomes]
rs60578339	1.00[AMR][1000 genomes]
rs6545043	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap]
rs6545044	1.00[CEU][hapmap]
rs6715766	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6756820	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7355307	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs7557764	1.00[EUR][1000 genomes]
rs7577850	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7608588	1.00[CEU][hapmap];1.00[YRI][hapmap]

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	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48668600-48682000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:48668800-48678800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:48668800-48679600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr2:48668800-48682400	Weak transcription	Lung	lung
5	chr2:48669000-48678400	Weak transcription	Colonic Mucosa	Colon
6	chr2:48669000-48678800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr2:48669000-48679000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:48669000-48680000	Weak transcription	Fetal Stomach	stomach
9	chr2:48669000-48681800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:48669000-48683400	Weak transcription	Right Ventricle	heart
11	chr2:48669200-48678400	Weak transcription	HUVEC	blood vessel
12	chr2:48669200-48698200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:48669400-48685000	Weak transcription	Fetal Brain Female	brain
14	chr2:48669400-48693800	Weak transcription	Hela-S3	cervix
15	chr2:48669600-48694200	Weak transcription	Fetal Brain Male	brain
16	chr2:48670000-48679000	Weak transcription	Brain Germinal Matrix	brain
17	chr2:48670400-48678200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:48670400-48678800	Weak transcription	Fetal Muscle Leg	muscle
19	chr2:48670400-48678800	Weak transcription	Ovary	ovary
20	chr2:48670800-48681800	Weak transcription	Gastric	stomach
21	chr2:48670800-48681800	Weak transcription	Spleen	Spleen
22	chr2:48671400-48678200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:48671600-48681800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:48671800-48677200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:48671800-48678600	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr2:48671800-48692400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr2:48672800-48677800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:48673000-48678600	Weak transcription	Placenta	Placenta
29	chr2:48673000-48679000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:48673000-48681600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:48673000-48681800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:48673000-48682000	Weak transcription	Esophagus	oesophagus
33	chr2:48673000-48686800	Weak transcription	Pancreas	Pancrea
34	chr2:48673000-48697400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:48673200-48679200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr2:48673200-48724000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:48673600-48677200	Weak transcription	Aorta	Aorta
38	chr2:48673600-48679000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:48673600-48679000	Weak transcription	Left Ventricle	heart
40	chr2:48674000-48677600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:48674200-48677200	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr2:48674200-48679200	Enhancers	K562	blood
43	chr2:48674400-48677000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr2:48674400-48677200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:48674400-48678200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:48674600-48677200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:48674600-48678400	Enhancers	Brain Hippocampus Middle	brain
48	chr2:48674800-48677000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:48674800-48678800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:48674800-48687000	Weak transcription	Small Intestine	intestine

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