Variant report

Variant	rs1056445
Chromosome Location	chr2:55490819-55490820
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55489175..55493124-chr2:55494672..55498680,8	MCF-7	breast:
2	chr2:55458825..55461494-chr2:55489314..55491027,2	MCF-7	breast:
3	chr2:55490801..55492846-chr2:55494879..55496493,2	K562	blood:
4	chr2:55481797..55485521-chr2:55489463..55492846,3	K562	blood:

Variant related genes	Relation type
ENSG00000162994	Chromatin interaction
ENSG00000085760	Chromatin interaction
ENSG00000143947	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10193886	0.86[YRI][hapmap]
rs10200120	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10200424	0.86[YRI][hapmap]
rs11357	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12052613	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1437393	0.81[LWK][hapmap];0.86[YRI][hapmap]
rs2576711	0.90[CHD][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];0.93[MKK][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2576712	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2576719	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2576721	0.84[AFR][1000 genomes]
rs2589080	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2589092	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589093	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589094	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2589096	0.90[CHD][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2589100	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2864819	0.87[ASN][1000 genomes]
rs2864826	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2917779	0.82[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920967	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34348115	0.81[CHB][hapmap];0.89[CHD][hapmap]
rs34511570	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4435493	0.91[CHB][hapmap];0.87[CHD][hapmap]
rs55997390	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56039135	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56384563	0.83[ASN][1000 genomes]
rs62135146	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6545477	0.83[YRI][hapmap]
rs6545480	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6711753	0.83[YRI][hapmap]
rs6727118	0.86[YRI][hapmap]
rs6727131	0.83[YRI][hapmap]
rs6737227	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6747364	0.83[YRI][hapmap]
rs6755515	0.83[ASN][1000 genomes]
rs72799507	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7580936	0.81[EUR][1000 genomes]
rs7597293	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs934709	0.95[CHB][hapmap];0.89[CHD][hapmap]
rs9677948	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3502708	chr2:55481350-55506212	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3502709	chr2:55481350-55506212	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv525025	chr2:55483020-55505456	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1056445	MTIF2	cis	multi-tissue	Pritchard
rs1056445	C2orf63	cis	lymphoblastoid	seeQTL
rs1056445	CLHC1	cis	Adipose Subcutaneous	GTEx
rs1056445	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs1056445	CLHC1	cis	Artery Tibial	GTEx
rs1056445	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55461600-55495400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:55461600-55495400	Weak transcription	Stomach Mucosa	stomach
3	chr2:55461800-55493400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:55461800-55495000	Weak transcription	Fetal Brain Male	brain
5	chr2:55462000-55493200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr2:55463000-55495400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:55463800-55494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:55463800-55495600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:55464600-55495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:55465600-55494400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:55466000-55493200	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr2:55468200-55493400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:55468400-55493200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:55468400-55494400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:55468600-55494400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:55468800-55493600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:55468800-55494400	Strong transcription	Adipose Nuclei	Adipose
18	chr2:55468800-55494400	Strong transcription	Liver	Liver
19	chr2:55469400-55492600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:55470800-55494200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:55472000-55495200	Weak transcription	Psoas Muscle	Psoas
22	chr2:55476000-55495400	Weak transcription	HUVEC	blood vessel
23	chr2:55476600-55495400	Weak transcription	Aorta	Aorta
24	chr2:55476600-55495400	Weak transcription	Fetal Heart	heart
25	chr2:55476600-55495600	Weak transcription	Esophagus	oesophagus
26	chr2:55476800-55495400	Weak transcription	Fetal Kidney	kidney
27	chr2:55478400-55493400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:55478400-55494800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:55478800-55494200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:55479000-55493400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:55480000-55495400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:55480400-55495600	Weak transcription	Brain Substantia Nigra	brain
33	chr2:55481400-55495400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr2:55481400-55495400	Weak transcription	Fetal Lung	lung
35	chr2:55481600-55495400	Weak transcription	NHDF-Ad	bronchial
36	chr2:55482800-55492000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr2:55482800-55492400	Strong transcription	Left Ventricle	heart
38	chr2:55482800-55494600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:55483000-55494400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr2:55483000-55494600	Strong transcription	Fetal Intestine Small	intestine
41	chr2:55483000-55494600	Strong transcription	Fetal Stomach	stomach
42	chr2:55483200-55494800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:55483800-55492200	Strong transcription	Fetal Intestine Large	intestine
44	chr2:55484000-55491800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:55484000-55493400	Strong transcription	HepG2	liver
46	chr2:55484000-55493600	Strong transcription	Placenta	Placenta
47	chr2:55484600-55492400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr2:55484600-55493400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:55484600-55493400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:55484600-55494400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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