Variant report

Variant	rs7302808
Chromosome Location	chr12:12420232-12420233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:492)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:492 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:12420151-12420448	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:12419561-12420520	A549	lung:	n/a	n/a
3	POLR2A	chr12:12419534-12420538	K562	blood:	n/a	n/a
4	MAZ	chr12:12419540-12420548	K562	blood:	n/a	chr12:12419896-12419906
5	RELA	chr12:12419819-12420548	GM18951	blood:	n/a	n/a
6	CREB1	chr12:12419649-12420403	K562	blood:	n/a	n/a
7	TAF7	chr12:12419574-12420562	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr12:12419732-12420539	GM12878	blood:	n/a	n/a
9	PAX5	chr12:12419714-12420364	GM12878	blood:	n/a	n/a
10	TEAD4	chr12:12419876-12420356	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:12419576-12420533	GM12878	blood:	n/a	n/a
12	PBX3	chr12:12419854-12420345	GM12878	blood:	n/a	n/a
13	GABPA	chr12:12420128-12420478	H1-hESC	embryonic stem cell:	n/a	n/a
14	TBP	chr12:12419624-12420999	K562	blood:	n/a	n/a
15	PAX5	chr12:12419786-12420498	GM12878	blood:	n/a	n/a
16	SIN3AK20	chr12:12419735-12420294	K562	blood:	n/a	n/a
17	FOXA2	chr12:12419815-12420616	A549	lung:	n/a	n/a
18	MAX	chr12:12419181-12420615	HepG2	liver:	n/a	chr12:12419896-12419906
19	MAX	chr12:12419699-12420517	K562	blood:	n/a	chr12:12419896-12419906
20	POLR2A	chr12:12419658-12420476	A549	lung:	n/a	n/a
21	TAF1	chr12:12419413-12421039	H1-neurons	neurons:	n/a	n/a
22	MYC	chr12:12419839-12420414	MCF-7	breast:	n/a	chr12:12419896-12419906
23	JUND	chr12:12420152-12420445	H1-hESC	embryonic stem cell:	n/a	n/a
24	ATF3	chr12:12419668-12420553	A549	lung:	n/a	n/a
25	YY1	chr12:12420146-12420499	H1-hESC	embryonic stem cell:	n/a	chr12:12420314-12420328 chr12:12420311-12420325 chr12:12420370-12420381 chr12:12420313-12420322
26	POLR2A	chr12:12419669-12420488	SK-N-MC	brain:	n/a	n/a
27	MAX	chr12:12419162-12421115	ECC-1	luminal epithelium:	n/a	chr12:12419896-12419906
28	SIN3AK20	chr12:12420149-12420415	HepG2	liver:	n/a	n/a
29	POLR2A	chr12:12419695-12420535	GM18951	blood:	n/a	n/a
30	RAD21	chr12:12420120-12420631	SK-N-SH_RA	brain:	n/a	chr12:12420311-12420325 chr12:12420152-12420166
31	KAP1	chr12:12419888-12420558	HEK293	kidney:	n/a	n/a
32	MAX	chr12:12419736-12420513	SK-N-SH	brain:	n/a	chr12:12419896-12419906
33	POLR2A	chr12:12419607-12420621	IMR90	lung:	n/a	n/a
34	FOXA2	chr12:12419882-12420364	HepG2	liver:	n/a	n/a
35	MAX	chr12:12420153-12420418	K562	blood:	n/a	n/a
36	CTCF	chr12:12420180-12420330	HBMEC	blood vessel:	n/a	n/a
37	POLR2A	chr12:12419650-12420555	GM19193	blood:	n/a	n/a
38	TCF12	chr12:12420153-12420458	GM12878	blood:	n/a	chr12:12420327-12420337
39	MYC	chr12:12419758-12420441	MCF-7	breast:	n/a	chr12:12419896-12419906
40	TAF1	chr12:12419755-12420723	A549	lung:	n/a	n/a
41	RAD21	chr12:12419728-12421034	HepG2	liver:	n/a	chr12:12420311-12420325 chr12:12420961-12420970 chr12:12420152-12420166
42	POLR2A	chr12:12419558-12420524	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr12:12420052-12420464	GM12892	blood:	n/a	n/a
44	IRF4	chr12:12419831-12420274	GM12878	blood:	n/a	n/a
45	POLR2A	chr12:12419709-12420540	GM12878	blood:	n/a	n/a
46	TCF7L2	chr12:12419815-12420582	PANC-1	pancreas:	n/a	n/a
47	MXI1	chr12:12418537-12420523	Hela-S3	cervix:	n/a	chr12:12420328-12420337
48	ZBTB7A	chr12:12418922-12420599	ECC-1	luminal epithelium:	n/a	chr12:12420349-12420358
49	TEAD4	chr12:12419613-12420711	ECC-1	luminal epithelium:	n/a	n/a
50	RELA	chr12:12419839-12420629	GM18505	blood:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:12419582..12421306-chr12:12876017..12878198,2	MCF-7	breast:
2	chr12:12378227..12379810-chr12:12418939..12421766,2	K562	blood:
3	chr12:12419134..12421122-chr12:12441823..12443690,2	MCF-7	breast:
4	chr12:12400936..12406172-chr12:12417674..12422348,4	K562	blood:
5	chr12:12229163..12231212-chr12:12420011..12422255,2	K562	blood:
6	chr12:12390182..12397827-chr12:12417123..12421502,7	MCF-7	breast:
7	chr12:12419370..12422118-chr12:12510348..12512093,2	MCF-7	breast:
8	chr12:12393044..12397840-chr12:12419223..12421821,5	MCF-7	breast:
9	chr12:12230786..12232660-chr12:12419937..12421467,2	K562	blood:
10	chr12:12419774..12421330-chr12:12508637..12511348,2	MCF-7	breast:
11	chr12:12411626..12414518-chr12:12420226..12422396,2	K562	blood:
12	chr12:12401851..12404835-chr12:12418306..12421349,3	MCF-7	breast:
13	chr12:12419999..12420724-chr7:48018768..48019330,2	Hela-S3	cervix:
14	chr12:12399860..12402436-chr12:12417674..12420343,2	K562	blood:
15	chr12:12418062..12421378-chr12:12712958..12715949,4	MCF-7	breast:
16	chr12:12418888..12421558-chr12:12875681..12878464,3	MCF-7	breast:
17	chr12:12223594..12226384-chr12:12419195..12421286,2	MCF-7	breast:
18	chr12:12419781..12420755-chr17:33569952..33570461,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
LRP6	TF binding region
ENSG00000199551	Chromatin interaction
ENSG00000207010	Chromatin interaction
ENSG00000070018	Chromatin interaction
ENSG00000266947	Chromatin interaction
ENSG00000136273	Chromatin interaction
ENSG00000256658	Chromatin interaction
ENSG00000165714	Chromatin interaction
ENSG00000205791	Chromatin interaction
ENSG00000121380	Chromatin interaction
ENSG00000270857	Chromatin interaction
ENSG00000166750	Chromatin interaction
ENSG00000111266	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10431302	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10431304	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10772540	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10772546	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10845494	0.81[EUR][1000 genomes]
rs10845495	0.82[EUR][1000 genomes]
rs10845501	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10845507	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11054731	0.82[EUR][1000 genomes]
rs11054754	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12366664	0.81[EUR][1000 genomes]
rs12823243	0.81[EUR][1000 genomes]
rs1819871	0.83[EUR][1000 genomes]
rs2417086	0.81[EUR][1000 genomes]
rs4763785	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4763794	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4763795	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61920859	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6488507	0.80[EUR][1000 genomes]
rs7956548	0.81[EUR][1000 genomes]
rs7956971	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7962366	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7965201	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7975772	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7979447	0.81[EUR][1000 genomes]
rs7979787	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9300240	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
4	nsv832332	chr12:12344027-12484966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12416800-12420600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:12416800-12420600	Active TSS	GM12878-XiMat	blood
3	chr12:12417200-12420600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr12:12417400-12420600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:12417600-12420600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr12:12417600-12420800	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr12:12417600-12420800	Active TSS	HSMMtube	muscle
8	chr12:12417800-12420400	Active TSS	Fetal Muscle Leg	muscle
9	chr12:12417800-12420600	Active TSS	H1 Cell Line	embryonic stem cell
10	chr12:12417800-12420600	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr12:12417800-12420600	Active TSS	Colon Smooth Muscle	Colon
12	chr12:12417800-12420600	Active TSS	Fetal Lung	lung
13	chr12:12417800-12420600	Active TSS	Fetal Stomach	stomach
14	chr12:12417800-12420600	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr12:12417800-12420800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:12417800-12420800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:12417800-12420800	Active TSS	Fetal Brain Male	brain
18	chr12:12417800-12420800	Active TSS	Left Ventricle	heart
19	chr12:12417800-12420800	Active TSS	Psoas Muscle	Psoas
20	chr12:12417800-12420800	Active TSS	NHDF-Ad	bronchial
21	chr12:12417800-12421000	Active TSS	Aorta	Aorta
22	chr12:12417800-12421000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:12417800-12421000	Active TSS	Right Atrium	heart
24	chr12:12418000-12420600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:12418000-12420600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:12418000-12420600	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr12:12418000-12420600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:12418000-12420600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:12418000-12420600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:12418000-12420600	Active TSS	Fetal Kidney	kidney
31	chr12:12418000-12420600	Active TSS	Stomach Mucosa	stomach
32	chr12:12418000-12420600	Active TSS	A549	lung
33	chr12:12418000-12420600	Active TSS	HMEC	breast
34	chr12:12418000-12420600	Active TSS	K562	blood
35	chr12:12418000-12420600	Active TSS	NHLF	lung
36	chr12:12418000-12420800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:12418000-12420800	Active TSS	Fetal Intestine Large	intestine
38	chr12:12418000-12420800	Active TSS	Ovary	ovary
39	chr12:12418000-12421000	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr12:12418000-12421000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:12418000-12421000	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr12:12418000-12421200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:12418200-12420400	Active TSS	Liver	Liver
44	chr12:12418200-12420400	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr12:12418200-12420600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:12418200-12420600	Active TSS	Brain Anterior Caudate	brain
47	chr12:12418200-12420600	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr12:12418200-12420600	Active TSS	Rectal Smooth Muscle	rectum
49	chr12:12418200-12420800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:12418200-12420800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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