Variant report

Variant	rs2117029
Chromosome Location	chr12:49408440-49408441
allele	A/T
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	chr12:49245310..49247176-chr12:49407825..49409649,2	MCF-7	breast:
2	chr12:49408415..49414757-chr12:49522619..49525582,9	MCF-7	breast:
3	chr12:49408338..49419708-chr12:49447252..49460551,38	K562	blood:
4	chr12:49408247..49410233-chr12:49503359..49505621,2	MCF-7	breast:
5	chr12:49406834..49409203-chr12:49502469..49504169,2	K562	blood:
6	chr12:49402719..49406068-chr12:49407016..49408969,3	MCF-7	breast:
7	chr12:49322957..49325651-chr12:49408385..49410864,2	MCF-7	breast:
8	chr12:49407466..49416688-chr12:49451532..49456163,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000139636	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000123416	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10459221	0.81[ASN][1000 genomes]
rs10459232	0.81[CEU][hapmap];0.81[ASN][1000 genomes]
rs1054442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10747559	0.86[ASN][1000 genomes]
rs10783299	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783300	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783301	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875906	0.94[ASN][1000 genomes]
rs10875908	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875910	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10875911	1.00[ASN][1000 genomes]
rs10875912	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10875913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875914	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875917	0.81[ASN][1000 genomes]
rs10875918	0.80[ASN][1000 genomes]
rs11168822	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168827	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168838	0.83[ASN][1000 genomes]
rs11168839	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168850	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1138908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12580349	0.83[CHB][hapmap];0.86[ASN][1000 genomes]
rs12821008	0.80[ASN][1000 genomes]
rs2241726	0.96[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2293445	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293446	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2304275	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34436857	0.90[ASN][1000 genomes]
rs3741619	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3741622	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3782357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580698	0.80[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6580699	0.80[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7296288	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs7300136	0.80[ASN][1000 genomes]
rs7969091	0.80[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs876333	0.96[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	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2117029	RP11-386G11.3	cis	Muscle Skeletal	GTEx
rs2117029	RP11-386G11.5	cis	Muscle Skeletal	GTEx
rs2117029	DDN	cis	Muscle Skeletal	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49395400-49411600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr12:49396000-49411600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:49396800-49411400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:49397000-49411200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:49397000-49411400	Weak transcription	Fetal Brain Male	brain
6	chr12:49397200-49411600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:49397600-49411400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:49399200-49411400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:49399600-49411000	Weak transcription	Pancreas	Pancrea
10	chr12:49399800-49411000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:49399800-49411400	Weak transcription	Fetal Kidney	kidney
12	chr12:49399800-49411600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:49400000-49410200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:49403200-49411400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:49404200-49408600	Strong transcription	GM12878-XiMat	blood
16	chr12:49404200-49411400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:49405200-49410600	Weak transcription	NHDF-Ad	bronchial
18	chr12:49405400-49410000	Weak transcription	NHEK	skin
19	chr12:49406000-49408600	Strong transcription	A549	lung
20	chr12:49406000-49408600	Strong transcription	Hela-S3	cervix
21	chr12:49406000-49411600	Weak transcription	Colonic Mucosa	Colon
22	chr12:49406000-49411600	Weak transcription	Esophagus	oesophagus
23	chr12:49406200-49411200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:49406200-49411400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:49406200-49411600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:49406200-49411600	Weak transcription	Aorta	Aorta
27	chr12:49406200-49411800	Weak transcription	Lung	lung
28	chr12:49406400-49411200	Weak transcription	Brain Germinal Matrix	brain
29	chr12:49406600-49408800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:49406600-49411000	Weak transcription	Fetal Intestine Small	intestine
31	chr12:49406600-49411600	Weak transcription	Spleen	Spleen
32	chr12:49406600-49411800	Weak transcription	Gastric	stomach
33	chr12:49406800-49410200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr12:49406800-49410200	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr12:49406800-49410600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:49406800-49410600	Weak transcription	Brain Angular Gyrus	brain
37	chr12:49406800-49411000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:49406800-49411000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr12:49406800-49411200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr12:49406800-49411200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr12:49406800-49411200	Weak transcription	HUVEC	blood vessel
42	chr12:49406800-49411400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:49406800-49411400	Weak transcription	Primary B cells from cord blood	blood
44	chr12:49406800-49411400	Weak transcription	Brain Anterior Caudate	brain
45	chr12:49406800-49411400	Weak transcription	Brain Substantia Nigra	brain
46	chr12:49406800-49411400	Weak transcription	Small Intestine	intestine
47	chr12:49407000-49409800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr12:49407000-49410000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:49407000-49410000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr12:49407000-49410200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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