Variant report

Variant	rs28673982
Chromosome Location	chr12:124016464-124016465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr12:124016287-124016755	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:124016415-124017057	HUVEC	blood vessel:	n/a	n/a
3	RUNX3	chr12:124016461-124017071	GM12878	blood:	n/a	n/a
4	RUNX3	chr12:124016450-124017068	GM12878	blood:	n/a	n/a
5	SPI1	chr12:124016301-124017227	GM12878	blood:	n/a	chr12:124016835-124016844 chr12:124016837-124016850
6	RCOR1	chr12:124016450-124016789	K562	blood:	n/a	n/a
7	RCOR1	chr12:124016438-124018290	IMR90	lung:	n/a	n/a
8	ZNF143	chr12:124016291-124016930	K562	blood:	n/a	n/a
9	BHLHE40	chr12:124016448-124016532	K562	blood:	n/a	n/a
10	POLR2A	chr12:124014798-124016776	K562	blood:	n/a	n/a
11	POLR2A	chr12:124016405-124016771	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:123955912..123957787-chr12:124014886..124016796,2	K562	blood:
2	chr12:124015709..124018064-chr12:124066858..124069100,3	MCF-7	breast:
3	chr12:123947470..123950375-chr12:124015636..124018854,3	K562	blood:
4	chr12:124006455..124008310-chr12:124016022..124017705,2	K562	blood:
5	chr12:124014934..124016748-chr12:124100287..124103243,2	MCF-7	breast:
6	chr12:123753293..123757508-chr12:124015727..124020202,5	K562	blood:
7	chr12:124015786..124020200-chr12:124020787..124024805,6	K562	blood:
8	chr12:123942564..123944577-chr12:124016063..124019666,4	MCF-7	breast:
9	chr12:123873494..123875550-chr12:124015653..124017169,2	MCF-7	breast:
10	chr12:124014995..124016623-chr12:124054786..124056310,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR3908	TF binding region
ENSG00000206897	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000266655	Chromatin interaction
ENSG00000184209	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1057879	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs10773019	1.00[JPT][hapmap]
rs10846526	0.85[ASN][1000 genomes]
rs10846530	1.00[JPT][hapmap]
rs10846531	0.82[GIH][hapmap];0.91[MEX][hapmap]
rs12308953	1.00[JPT][hapmap]
rs12309685	1.00[JPT][hapmap]
rs12313119	1.00[JPT][hapmap]
rs2048615	0.85[ASN][1000 genomes]
rs2063629	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2333831	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs28371124	0.85[ASN][1000 genomes]
rs28403439	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28430750	0.85[ASN][1000 genomes]
rs28454032	0.86[ASN][1000 genomes]
rs28465339	0.85[ASN][1000 genomes]
rs28478446	0.85[ASN][1000 genomes]
rs28497190	0.85[ASN][1000 genomes]
rs28535724	1.00[ASN][1000 genomes]
rs28539789	0.85[ASN][1000 genomes]
rs28654896	0.85[ASN][1000 genomes]
rs28701527	0.85[ASN][1000 genomes]
rs28707421	0.85[ASN][1000 genomes]
rs28711456	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28712858	0.85[ASN][1000 genomes]
rs28741988	0.85[ASN][1000 genomes]
rs28758342	0.85[ASN][1000 genomes]
rs3748268	0.91[MEX][hapmap]
rs4930716	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5027860	0.86[ASN][1000 genomes]
rs59560692	0.82[ASN][1000 genomes]
rs61953537	0.88[ASN][1000 genomes]
rs61953538	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61953539	1.00[ASN][1000 genomes]
rs61953543	1.00[ASN][1000 genomes]
rs61953552	0.85[ASN][1000 genomes]
rs61953557	0.85[ASN][1000 genomes]
rs6488879	0.85[CEU][hapmap]
rs71458805	0.81[ASN][1000 genomes]
rs7307227	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7313179	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7358562	1.00[JPT][hapmap]
rs786455	0.88[CEU][hapmap]
rs7965334	0.86[ASN][1000 genomes]
rs883503	0.88[CEU][hapmap]
rs884892	0.91[MEX][hapmap]
rs9697379	0.88[CEU][hapmap]
rs9697543	0.90[ASN][1000 genomes]
rs9697721	0.90[ASN][1000 genomes]
rs9723048	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1037260	chr12:123956749-124023069	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	nsv560495	chr12:124012974-124017461	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs28673982	RP11-486O12.2	cis	Thyroid	GTEx
rs28673982	PXN	cis	cerebellum	SCAN
rs28673982	DDX55	cis	cerebellum	SCAN
rs28673982	TCTN2	cis	cerebellum	SCAN
rs28673982	DDX55	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124001200-124017400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:124001400-124017400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:124002000-124016800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:124004600-124016800	Weak transcription	Stomach Mucosa	stomach
5	chr12:124004800-124016600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:124005800-124016600	Weak transcription	Fetal Kidney	kidney
7	chr12:124006200-124017600	Weak transcription	Small Intestine	intestine
8	chr12:124006800-124016800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:124007200-124016600	Weak transcription	Primary T cells from cord blood	blood
10	chr12:124007800-124016600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:124007800-124017000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:124007800-124017400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:124008000-124017000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:124008000-124017400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:124008200-124016600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr12:124008200-124017200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:124008400-124016600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:124008400-124017400	Weak transcription	Gastric	stomach
19	chr12:124009200-124016600	Weak transcription	Lung	lung
20	chr12:124009200-124016600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:124009400-124016600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:124011000-124016600	Strong transcription	Fetal Intestine Small	intestine
23	chr12:124012000-124016600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:124013000-124016600	Weak transcription	HSMMtube	muscle
25	chr12:124014000-124016600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:124014400-124016800	Genic enhancers	Fetal Heart	heart
27	chr12:124014600-124016600	Weak transcription	NHLF	lung
28	chr12:124015000-124016600	Enhancers	Brain Anterior Caudate	brain
29	chr12:124015000-124016600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:124015000-124016600	Genic enhancers	Fetal Muscle Leg	muscle
31	chr12:124015000-124016600	Strong transcription	A549	lung
32	chr12:124015000-124016800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:124015000-124016800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr12:124015200-124017000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:124015200-124017200	Genic enhancers	Fetal Stomach	stomach
36	chr12:124015200-124017400	Enhancers	Pancreas	Pancrea
37	chr12:124015400-124016600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
38	chr12:124015400-124016600	Enhancers	Brain Germinal Matrix	brain
39	chr12:124015400-124016600	Enhancers	Fetal Brain Male	brain
40	chr12:124015400-124016600	Enhancers	Rectal Smooth Muscle	rectum
41	chr12:124015400-124016600	Enhancers	HepG2	liver
42	chr12:124015400-124017000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:124015400-124018000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr12:124015600-124016800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
45	chr12:124015800-124016600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:124015800-124016600	Weak transcription	Aorta	Aorta
47	chr12:124015800-124016600	Enhancers	Placenta	Placenta
48	chr12:124015800-124016600	Enhancers	Psoas Muscle	Psoas
49	chr12:124015800-124016800	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr12:124015800-124016800	Enhancers	Ovary	ovary

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