Variant report

Variant	rs74060996
Chromosome Location	chr12:11698867-11698868
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr12:11698247-11699429	GM12878	blood:	n/a	n/a
2	BCLAF1	chr12:11698403-11699413	GM12878	blood:	n/a	chr12:11698542-11698549
3	POLR2A	chr12:11698807-11699047	GM12878	blood:	n/a	n/a
4	TAF1	chr12:11698636-11699298	GM12878	blood:	n/a	n/a
5	EP300	chr12:11698387-11699394	GM12878	blood:	n/a	chr12:11698398-11698412
6	MAZ	chr12:11698397-11699380	GM12878	blood:	n/a	chr12:11698586-11698596
7	POLR2A	chr12:11698759-11699372	GM12892	blood:	n/a	n/a
8	MEF2A	chr12:11698639-11699372	GM12878	blood:	n/a	chr12:11699108-11699116
9	ZEB1	chr12:11698765-11699151	GM12878	blood:	n/a	n/a
10	FOXM1	chr12:11698362-11699332	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:11698471-11699484	GM12878	blood:	n/a	n/a
12	NFIC	chr12:11698330-11699462	GM12878	blood:	n/a	n/a
13	ETS1	chr12:11698609-11699214	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:11698733-11699060	GM12891	blood:	n/a	n/a
15	WRNIP1	chr12:11698433-11699313	GM12878	blood:	n/a	n/a
16	ATF2	chr12:11698316-11699382	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:11698323-11699182	GM12892	blood:	n/a	n/a
18	NFIC	chr12:11698267-11699498	GM12878	blood:	n/a	n/a
19	SPI1	chr12:11698203-11699318	GM12878	blood:	n/a	chr12:11698578-11698591
20	PAX5	chr12:11698726-11699333	GM12878	blood:	n/a	n/a
21	SP1	chr12:11698356-11699400	GM12878	blood:	n/a	chr12:11698513-11698520 chr12:11698580-11698594
22	NFYB	chr12:11698710-11699386	GM12878	blood:	n/a	n/a
23	RUNX3	chr12:11698197-11699468	GM12878	blood:	n/a	n/a
24	STAT5A	chr12:11698156-11699428	GM12878	blood:	n/a	chr12:11698197-11698209 chr12:11698578-11698590
25	POLR2A	chr12:11698404-11699303	GM12892	blood:	n/a	n/a
26	SP1	chr12:11698429-11699383	GM12878	blood:	n/a	chr12:11698513-11698520 chr12:11698580-11698594
27	TBP	chr12:11698399-11699342	GM12878	blood:	n/a	n/a
28	RCOR1	chr12:11698459-11699290	GM12878	blood:	n/a	n/a
29	YY1	chr12:11698708-11699175	GM12878	blood:	n/a	n/a
30	TCF3	chr12:11698740-11699094	GM12878	blood:	n/a	n/a
31	BCLAF1	chr12:11698375-11699440	GM12878	blood:	n/a	chr12:11698542-11698549
32	BCL11A	chr12:11698793-11699268	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:11698493-11699019	GM12878	blood:	n/a	n/a
34	RELA	chr12:11698361-11699337	GM19099	blood:	n/a	n/a
35	FOXM1	chr12:11698572-11699473	GM12878	blood:	n/a	n/a
36	TBL1XR1	chr12:11698604-11699414	GM12878	blood:	n/a	n/a
37	MTA3	chr12:11698144-11699512	GM12878	blood:	n/a	n/a
38	POLR2A	chr12:11698265-11699492	GM12878	blood:	n/a	n/a
39	MTA3	chr12:11698276-11699433	GM12878	blood:	n/a	n/a
40	EBF1	chr12:11698729-11699348	GM12878	blood:	n/a	n/a
41	PAX5	chr12:11698681-11699279	GM12878	blood:	n/a	n/a
42	GATA3	chr12:11698544-11698979	SH-SY5Y	brain:	n/a	chr12:11698866-11698876 chr12:11698577-11698587
43	PML	chr12:11698249-11699514	GM12878	blood:	n/a	n/a
44	PAX5	chr12:11698233-11699410	GM12878	blood:	n/a	n/a
45	ETS1	chr12:11698414-11699302	GM12878	blood:	n/a	chr12:11698523-11698537
46	EBF1	chr12:11698353-11698940	GM12878	blood:	n/a	n/a
47	CREB1	chr12:11698283-11699435	GM12878	blood:	n/a	n/a
48	STAT5A	chr12:11698666-11699266	GM12878	blood:	n/a	n/a
49	CTCF	chr12:11698760-11698910	GM12872	blood:	n/a	n/a
50	PAX5	chr12:11698739-11698960	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000247157	TF binding region
RNU7-60P	TF binding region
ENSG00000221128	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10772486	0.87[ASN][1000 genomes]
rs11054341	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17817352	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2416791	0.86[ASN][1000 genomes]
rs2416792	0.87[ASN][1000 genomes]
rs4763703	0.89[ASN][1000 genomes]
rs4763705	0.86[ASN][1000 genomes]
rs6488425	0.88[ASN][1000 genomes]
rs6488426	0.89[ASN][1000 genomes]
rs6488427	0.88[ASN][1000 genomes]
rs6488428	0.86[ASN][1000 genomes]
rs7956437	0.87[ASN][1000 genomes]
rs7960374	0.87[ASN][1000 genomes]
rs7967647	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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	esv2758294	chr12:10969620-11714921	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv2759879	chr12:10969620-11714921	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv428272	chr12:11069845-11714921	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv469112	chr12:11575570-11711690	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv557573	chr12:11575570-11711690	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11695800-11700000	Enhancers	Fetal Stomach	stomach
2	chr12:11696200-11699800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr12:11696400-11700200	Enhancers	Primary hematopoietic stem cells	blood
4	chr12:11696800-11699400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:11696800-11699600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:11696800-11699800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:11697200-11699200	Weak transcription	Brain Anterior Caudate	brain
8	chr12:11697200-11699800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:11697200-11699800	Weak transcription	Fetal Intestine Small	intestine
10	chr12:11697400-11699400	Flanking Active TSS	Dnd41	blood
11	chr12:11697400-11699800	Enhancers	Primary B cells from peripheral blood	blood
12	chr12:11697400-11708600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:11697600-11699000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:11697800-11700000	Weak transcription	Esophagus	oesophagus
15	chr12:11698000-11699600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:11698200-11699000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr12:11698200-11699000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:11698200-11699000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:11698200-11699000	Flanking Active TSS	Fetal Thymus	thymus
20	chr12:11698200-11699200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr12:11698200-11699200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr12:11698200-11699200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:11698200-11699200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:11698200-11699200	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr12:11698200-11699400	Enhancers	Duodenum Mucosa	Duodenum
26	chr12:11698200-11699600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr12:11698200-11699600	Flanking Active TSS	GM12878-XiMat	blood
28	chr12:11698200-11699800	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr12:11698200-11699800	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr12:11698200-11700000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr12:11698200-11700000	Enhancers	NH-A	brain
32	chr12:11698200-11700800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr12:11698400-11699000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:11698400-11699000	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr12:11698400-11699000	Enhancers	Fetal Lung	lung
36	chr12:11698400-11699000	Enhancers	Left Ventricle	heart
37	chr12:11698400-11699000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr12:11698400-11699200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr12:11698400-11699200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:11698400-11699200	Enhancers	H9 Cell Line	embryonic stem cell
41	chr12:11698400-11699200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr12:11698400-11699200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:11698400-11699200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:11698400-11699200	Enhancers	Stomach Smooth Muscle	stomach
45	chr12:11698400-11699200	Flanking Active TSS	Thymus	Thymus
46	chr12:11698400-11699400	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr12:11698400-11699400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr12:11698400-11699400	Enhancers	Spleen	Spleen
49	chr12:11698400-11699600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr12:11698400-11699600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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