Variant report

Variant	rs2290516
Chromosome Location	chr4:48908354-48908355
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	chr4:48907349..48910637-chr4:48932106..48935377,4	MCF-7	breast:
2	chr13:21714238..21715079-chr4:48907831..48908602,2	Hela-S3	cervix:
3	chr4:48907758..48909914-chr4:48938093..48940676,2	MCF-7	breast:
4	chr4:48907952..48908549-chr4:48945945..48946857,2	MCF-7	breast:
5	chr4:48899707..48901382-chr4:48907101..48909045,2	K562	blood:
6	chr4:48779823..48782624-chr4:48905090..48909886,4	MCF-7	breast:
7	chr4:48700525..48703151-chr4:48906796..48908721,2	MCF-7	breast:
8	chr4:48832331..48834187-chr4:48907329..48910001,2	MCF-7	breast:
9	chr4:48831616..48834377-chr4:48906971..48910422,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000145247	Chromatin interaction
ENSG00000252913	Chromatin interaction
ENSG00000075539	Chromatin interaction
ENSG00000251334	Chromatin interaction
ENSG00000150459	Chromatin interaction
ENSG00000109180	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10517231	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11727343	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs11733534	0.81[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.92[YRI][hapmap]
rs11734191	0.82[ASN][1000 genomes]
rs11737706	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12504699	0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs12512637	0.90[JPT][hapmap]
rs13142540	0.88[YRI][hapmap]
rs13146034	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13149083	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs13152270	0.83[ASN][1000 genomes]
rs1455940	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1463365	0.91[ASN][1000 genomes]
rs1554256	0.96[YRI][hapmap]
rs2085292	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2247481	0.82[CHB][hapmap];0.81[LWK][hapmap];0.83[YRI][hapmap]
rs2289065	0.80[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs2572345	0.84[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs2572350	0.81[GIH][hapmap];0.85[JPT][hapmap]
rs2605267	0.83[TSI][hapmap]
rs2712156	0.82[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs2712158	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs34730980	0.91[ASN][1000 genomes]
rs3761729	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap]
rs4694906	0.90[JPT][hapmap]
rs4695407	0.81[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs6447666	0.81[CEU][hapmap];0.81[CHB][hapmap];0.80[GIH][hapmap]
rs6447670	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs724598	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7654032	0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs7660206	0.84[YRI][hapmap]
rs7665209	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs7672280	0.85[EUR][1000 genomes]
rs7685360	0.87[ASN][1000 genomes]
rs7687992	0.85[ASN][1000 genomes]
rs9291326	0.82[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap]
rs9637562	0.80[ASN][1000 genomes]
rs9997920	0.82[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2290516	MGC45416	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48906800-48908400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr4:48907000-48908400	Flanking Active TSS	HMEC	breast
3	chr4:48907200-48908800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:48907400-48908400	Flanking Active TSS	Dnd41	blood
5	chr4:48907400-48909200	Active TSS	Brain Anterior Caudate	brain
6	chr4:48907600-48908400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:48907600-48908400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:48907600-48908400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
9	chr4:48907600-48908400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:48907600-48908400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr4:48907600-48908400	Flanking Active TSS	Liver	Liver
12	chr4:48907600-48908400	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr4:48907600-48908400	Flanking Active TSS	Fetal Thymus	thymus
14	chr4:48907600-48908400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr4:48907600-48908400	Enhancers	Spleen	Spleen
16	chr4:48907600-48908400	Flanking Active TSS	HUVEC	blood vessel
17	chr4:48907600-48908400	Flanking Active TSS	Osteobl	bone
18	chr4:48907600-48908800	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr4:48907600-48909000	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr4:48907600-48909200	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr4:48907600-48909200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:48907600-48909200	Active TSS	Fetal Kidney	kidney
23	chr4:48907600-48909200	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr4:48907800-48908400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:48907800-48908400	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr4:48907800-48908400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr4:48907800-48908400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:48907800-48908400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:48907800-48908400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr4:48907800-48908800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:48907800-48909000	Active TSS	Brain Cingulate Gyrus	brain
32	chr4:48907800-48909000	Active TSS	Fetal Intestine Large	intestine
33	chr4:48907800-48909000	Active TSS	Gastric	stomach
34	chr4:48907800-48909200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr4:48907800-48909200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:48907800-48909200	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr4:48907800-48909200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:48907800-48909200	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr4:48907800-48909200	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr4:48907800-48909200	Active TSS	Rectal Smooth Muscle	rectum
41	chr4:48907800-48909200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
42	chr4:48907800-48909400	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr4:48907800-48909400	Active TSS	Stomach Smooth Muscle	stomach
44	chr4:48908000-48908400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr4:48908000-48908400	Flanking Active TSS	Primary B cells from peripheral blood	blood
46	chr4:48908000-48908400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:48908000-48908400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:48908000-48908400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:48908000-48908400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:48908000-48908400	Flanking Active TSS	Brain Hippocampus Middle	brain

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