Variant report

Variant	rs2292919
Chromosome Location	chr3:140661474-140661475
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:140659457..140662013-chr3:140675174..140679419,5	K562	blood:
2	chr3:140658799..140662032-chr3:140683166..140686698,4	MCF-7	breast:
3	chr20:52224635..52226312-chr3:140659938..140662134,2	MCF-7	breast:
4	chr3:140659978..140662148-chr3:140682890..140685821,2	MCF-7	breast:
5	chr3:140658725..140662722-chr3:140687297..140693458,7	MCF-7	breast:
6	chr17:56707856..56710618-chr3:140659373..140661853,2	MCF-7	breast:
7	chr3:140660122..140661654-chr3:140682941..140685773,2	K562	blood:
8	chr3:140657892..140662868-chr3:140689081..140692689,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction
ENSG00000235415	Chromatin interaction
ENSG00000114120	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000248773	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1047330	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1056126	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1056127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10935413	0.96[ASN][1000 genomes]
rs10935414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1109282	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1109283	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs11707116	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11710204	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11710926	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11711131	1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11713505	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11713816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11714438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11715248	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11717097	1.00[CEU][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes]
rs11717620	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11718040	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11718539	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11718563	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11720342	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12489397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1568337	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1593624	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16850915	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16850917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16850921	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16850924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16850926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2310859	0.87[ASN][1000 genomes]
rs2555702	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2555707	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2871615	0.85[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs35140461	0.98[ASN][1000 genomes]
rs3755764	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3755765	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3773835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3773837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3773838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4380393	0.88[EUR][1000 genomes]
rs4524250	0.95[ASN][1000 genomes]
rs57151068	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57526660	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57799705	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59128309	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59221985	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61052022	0.88[EUR][1000 genomes]
rs61151473	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61629363	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61708145	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6439962	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6770562	0.96[ASN][1000 genomes]
rs6785007	0.98[ASN][1000 genomes]
rs6810200	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs713354	0.86[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs72991025	0.95[EUR][1000 genomes]
rs72991046	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7621150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7626525	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7632043	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7637899	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs7638206	0.93[EUR][1000 genomes]
rs7643287	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7643434	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7643614	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7644725	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7649116	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7652381	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7653157	0.87[TSI][hapmap]
rs877142	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9880468	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591865	chr3:140396022-140728850	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1005522	chr3:140454632-140685915	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv536732	chr3:140454632-140685915	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv521218	chr3:140643038-140665147	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv3364537	chr3:140646303-140668571	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2292919	SLC25A36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140659400-140662200	Active TSS	Brain Angular Gyrus	brain
2	chr3:140659600-140663200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:140659600-140664600	Active TSS	GM12878-XiMat	blood
4	chr3:140659800-140662000	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr3:140659800-140662000	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr3:140659800-140662600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr3:140660000-140661600	Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr3:140660000-140661600	Active TSS	Adipose Nuclei	Adipose
9	chr3:140660000-140661800	Active TSS	Brain Substantia Nigra	brain
10	chr3:140660000-140661800	Active TSS	Duodenum Mucosa	Duodenum
11	chr3:140660000-140661800	Active TSS	Rectal Smooth Muscle	rectum
12	chr3:140660000-140661800	Active TSS	HUVEC	blood vessel
13	chr3:140660000-140661800	Active TSS	NH-A	brain
14	chr3:140660000-140662000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:140660000-140662000	Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr3:140660000-140662000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:140660000-140662000	Active TSS	Brain Anterior Caudate	brain
18	chr3:140660000-140662000	Active TSS	Brain Cingulate Gyrus	brain
19	chr3:140660000-140662000	Active TSS	Brain Hippocampus Middle	brain
20	chr3:140660000-140662000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:140660000-140662000	Active TSS	Fetal Brain Male	brain
22	chr3:140660000-140662000	Active TSS	Fetal Lung	lung
23	chr3:140660000-140662000	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr3:140660000-140662000	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr3:140660000-140662000	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr3:140660000-140662000	Active TSS	A549	lung
27	chr3:140660000-140662000	Active TSS	HSMMtube	muscle
28	chr3:140660000-140662200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:140660000-140662200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:140660000-140662200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:140660000-140662200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:140660000-140662200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:140660000-140662200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:140660000-140662200	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr3:140660000-140662200	Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr3:140660000-140662200	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr3:140660000-140662200	Active TSS	Placenta	Placenta
38	chr3:140660000-140662200	Active TSS	Thymus	Thymus
39	chr3:140660000-140662200	Active TSS	NHEK	skin
40	chr3:140660000-140662400	Active TSS	H9 Cell Line	embryonic stem cell
41	chr3:140660000-140662400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:140660000-140662400	Active TSS	Muscle Satellite Cultured Cells	--
43	chr3:140660000-140662400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:140660000-140662400	Active TSS	Brain Germinal Matrix	brain
45	chr3:140660000-140662400	Active TSS	Colonic Mucosa	Colon
46	chr3:140660000-140662400	Active TSS	Fetal Kidney	kidney
47	chr3:140660000-140662400	Active TSS	Fetal Stomach	stomach
48	chr3:140660000-140662600	Active TSS	H1 Cell Line	embryonic stem cell
49	chr3:140660000-140662600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:140660000-140662600	Active TSS	iPS-15b Cell Line	embryonic stem cell

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