Variant report

Variant	rs1169309
Chromosome Location	chr12:121439192-121439193
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:121437936-121439682	GM12892	blood:	n/a	n/a
2	POLR2A	chr12:121436979-121440697	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:121437788-121439775	K562	blood:	n/a	n/a
4	POLR2A	chr12:121438708-121439414	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr12:121438807-121439271	A549	lung:	n/a	n/a
6	POLR2A	chr12:121438788-121440811	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:121438700-121440279	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:121436588-121439769	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr12:121438511-121442806	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:121438699-121439275	GM12891	blood:	n/a	n/a
11	MYC	chr12:121439067-121439261	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr12:121437040-121439244	K562	blood:	n/a	n/a
13	POLR2A	chr12:121438718-121439196	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:121438311-121440243	GM12892	blood:	n/a	n/a
15	POLR2A	chr12:121438740-121439416	HL-60	blood:	n/a	n/a
16	POLR2A	chr12:121436209-121439885	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr12:121439021-121439473	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121429573..121435133-chr12:121436242..121441204,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000271769	TF binding region
ENSG00000135100	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1169300	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1169301	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1169306	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1169310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1169311	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1169312	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1169313	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1169314	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1169315	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1182933	0.95[ASN][1000 genomes]
rs2254971	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2257764	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2257962	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2259816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2259852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2264750	0.97[ASN][1000 genomes]
rs2264782	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464196	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4278584	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs735396	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv899561	chr12:121376416-121525591	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv1037195	chr12:121408540-121470375	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1039216	chr12:121421701-121538491	Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121418600-121441000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:121418800-121439400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:121419600-121441000	Weak transcription	Small Intestine	intestine
4	chr12:121426200-121440200	Strong transcription	HepG2	liver
5	chr12:121427600-121442600	Strong transcription	Fetal Intestine Large	intestine
6	chr12:121427800-121441200	Strong transcription	Fetal Intestine Small	intestine
7	chr12:121429800-121442000	Strong transcription	Duodenum Mucosa	Duodenum
8	chr12:121429800-121451600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr12:121431200-121439200	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr12:121431200-121440600	Weak transcription	Fetal Lung	lung
11	chr12:121432600-121441200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:121433200-121448200	Weak transcription	Fetal Kidney	kidney
13	chr12:121433600-121440600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:121435400-121441200	Weak transcription	HSMM	muscle
15	chr12:121435600-121439400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr12:121436000-121441200	Weak transcription	NHEK	skin
17	chr12:121436400-121439400	Weak transcription	NHLF	lung
18	chr12:121436400-121441200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:121436600-121440800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:121436600-121452800	Weak transcription	Fetal Heart	heart
21	chr12:121436800-121439200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:121436800-121441000	Weak transcription	Brain Angular Gyrus	brain
23	chr12:121436800-121441000	Weak transcription	HSMMtube	muscle
24	chr12:121436800-121442000	Weak transcription	GM12878-XiMat	blood
25	chr12:121436800-121442400	Weak transcription	Hela-S3	cervix
26	chr12:121437000-121440000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:121437000-121441000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:121437200-121439600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr12:121437200-121439600	Enhancers	Stomach Mucosa	stomach
30	chr12:121437200-121441000	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:121437200-121441200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr12:121437400-121439400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:121437400-121439400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr12:121437400-121439400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr12:121437400-121439400	Enhancers	Placenta	Placenta
36	chr12:121437400-121441200	Weak transcription	Primary B cells from cord blood	blood
37	chr12:121437400-121442800	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:121437600-121439200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr12:121437600-121439200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:121437600-121439200	Weak transcription	Brain Anterior Caudate	brain
41	chr12:121437600-121439200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr12:121437600-121439600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:121437600-121439800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:121437600-121439800	Enhancers	Fetal Thymus	thymus
45	chr12:121437600-121452000	Strong transcription	Fetal Stomach	stomach
46	chr12:121437600-121453000	Weak transcription	Fetal Brain Male	brain
47	chr12:121437600-121453600	Weak transcription	Right Atrium	heart
48	chr12:121437800-121439400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:121437800-121439400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr12:121437800-121439400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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