Variant report

Variant	rs34099549
Chromosome Location	chr12:124085062-124085063
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:124082857-124085456	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:124067363..124072745-chr12:124084857..124088217,7	K562	blood:
2	chr12:124084988..124092992-chr12:124114351..124121638,14	K562	blood:
3	chr12:123716942..123720349-chr12:124084108..124086499,3	K562	blood:
4	chr12:124017444..124019100-chr12:124084646..124086674,2	MCF-7	breast:
5	chr12:124084914..124087862-chr12:124122413..124125179,2	K562	blood:
6	chr12:124084893..124086565-chr12:124117453..124119818,2	K562	blood:
7	chr12:123755058..123757440-chr12:124084744..124087456,3	K562	blood:
8	chr12:124067302..124072457-chr12:124084684..124088760,8	K562	blood:
9	chr12:124084644..124087346-chr12:124096148..124098451,3	K562	blood:
10	chr12:124084509..124086598-chr12:124112180..124115159,2	K562	blood:

No data

Variant related genes	Relation type
DDX55	TF binding region
ENSG00000111361	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000188026	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000247373	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10082874	0.88[AMR][1000 genomes]
rs11057298	0.93[ASN][1000 genomes]
rs11057302	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057306	1.00[ASN][1000 genomes]
rs11610013	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615043	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11834369	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837236	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099981	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099986	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877365	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340691	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28691687	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3209852	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61678733	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488879	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6488881	0.81[AMR][1000 genomes]
rs7136101	0.81[AMR][1000 genomes]
rs7301377	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303554	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73414262	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs786428	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786429	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786431	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786432	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786433	1.00[ASN][1000 genomes]
rs786434	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786435	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786437	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs786438	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786439	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786450	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786455	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7954782	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7958153	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960812	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968040	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7970545	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971779	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952360	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS 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 miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs34099549	RP11-486O12.2	cis	Muscle Skeletal	GTEx
rs34099549	RP11-486O12.2	cis	Thyroid	GTEx
rs34099549	RP11-486O12.2	cis	Esophagus Mucosa	GTEx
rs34099549	DDX55	cis	lung	GTEx
rs34099549	DDX55	cis	Thyroid	GTEx
rs34099549	RP11-486O12.2	cis	Artery Aorta	GTEx
rs34099549	RP11-486O12.2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124070000-124085800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:124072200-124085800	Weak transcription	Small Intestine	intestine
3	chr12:124073800-124085200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:124073800-124085400	Weak transcription	Stomach Mucosa	stomach
5	chr12:124074200-124086000	Weak transcription	Fetal Heart	heart
6	chr12:124075200-124085600	Weak transcription	Right Ventricle	heart
7	chr12:124075200-124085800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:124075200-124086000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:124075200-124086000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:124076800-124085600	Weak transcription	Pancreas	Pancrea
11	chr12:124077000-124085600	Weak transcription	Spleen	Spleen
12	chr12:124077000-124086200	Weak transcription	Aorta	Aorta
13	chr12:124077400-124086000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:124077400-124086000	Weak transcription	Fetal Brain Male	brain
15	chr12:124078400-124085600	Weak transcription	Esophagus	oesophagus
16	chr12:124078600-124085200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:124078600-124085400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:124079400-124085400	Weak transcription	Fetal Intestine Small	intestine
19	chr12:124079400-124085600	Weak transcription	Fetal Stomach	stomach
20	chr12:124079400-124085600	Weak transcription	Lung	lung
21	chr12:124080000-124085800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:124080600-124086000	Weak transcription	Ovary	ovary
23	chr12:124081800-124085400	Weak transcription	Colonic Mucosa	Colon
24	chr12:124081800-124085600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr12:124082000-124085400	Weak transcription	Primary B cells from cord blood	blood
26	chr12:124082000-124085600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:124082000-124086000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr12:124082200-124085400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:124082200-124085400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr12:124082200-124085400	Weak transcription	GM12878-XiMat	blood
31	chr12:124082200-124085600	Weak transcription	Brain Angular Gyrus	brain
32	chr12:124082200-124085600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:124082200-124085600	Weak transcription	Colon Smooth Muscle	Colon
34	chr12:124082200-124085600	Weak transcription	Fetal Muscle Leg	muscle
35	chr12:124082200-124085600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr12:124082200-124085800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:124082200-124086000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:124082400-124085200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr12:124082400-124085400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr12:124082400-124085400	Weak transcription	NHEK	skin
41	chr12:124082400-124085600	Weak transcription	Psoas Muscle	Psoas
42	chr12:124082400-124085800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:124082600-124085400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr12:124082800-124085600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr12:124082800-124085600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr12:124082800-124086000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr12:124083000-124085400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:124083000-124085600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:124083200-124085400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr12:124083200-124085400	Weak transcription	Hela-S3	cervix

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