Variant report

Variant	rs7953609
Chromosome Location	chr12:4429722-4429723
allele	A/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	MTA3	chr12:4429385-4430042	GM12878	blood:	n/a	n/a
2	CREB1	chr12:4429700-4430906	GM12878	blood:	n/a	n/a
3	TCF12	chr12:4429688-4430806	ECC-1	luminal epithelium:	n/a	chr12:4430174-4430181 chr12:4430655-4430665
4	TAF1	chr12:4429628-4430978	ECC-1	luminal epithelium:	n/a	n/a
5	TAF7	chr12:4429675-4430646	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr12:4429656-4430839	HUVEC	blood vessel:	n/a	n/a
7	FOXA2	chr12:4429672-4430213	A549	lung:	n/a	n/a
8	POLR2A	chr12:4429480-4431095	GM12891	blood:	n/a	n/a
9	POLR2A	chr12:4429526-4430997	GM12892	blood:	n/a	n/a
10	MAX	chr12:4429535-4430823	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr12:4429531-4430717	ECC-1	luminal epithelium:	n/a	n/a
12	SIN3AK20	chr12:4429652-4430823	MCF-7	breast:	n/a	n/a
13	POLR2A	chr12:4429550-4431036	GM12892	blood:	n/a	n/a
14	TCF7L2	chr12:4429639-4430512	HCT-116	colon:	n/a	n/a
15	RELA	chr12:4429636-4430896	GM15510	blood:	n/a	n/a
16	MXI1	chr12:4429314-4431278	SK-N-SH	brain:	n/a	n/a
17	SP1	chr12:4429677-4430744	A549	lung:	n/a	chr12:4430227-4430240 chr12:4430186-4430207 chr12:4430230-4430242 chr12:4430161-4430170 chr12:4430640-4430654 chr12:4430261-4430270 chr12:4430260-4430272 chr12:4430230-4430242 chr12:4430232-4430241 chr12:4430159-4430171 chr12:4430159-4430171 chr12:4430231-4430240 chr12:4430262-4430271
18	KAP1	chr12:4429654-4430918	HEK293	kidney:	n/a	n/a
19	CHD2	chr12:4429669-4430819	GM12878	blood:	n/a	n/a
20	TCF7L2	chr12:4429551-4430353	PANC-1	pancreas:	n/a	n/a
21	GATA1	chr12:4429697-4430634	K562	blood:	n/a	chr12:4430100-4430117 chr12:4430098-4430108 chr12:4430097-4430109 chr12:4430099-4430108 chr12:4430099-4430106
22	POLR2A	chr12:4429618-4430995	Hela-S3	cervix:	n/a	n/a
23	KAT2A	chr12:4429720-4430052	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr12:4429585-4430924	GM12892	blood:	n/a	n/a
25	MAZ	chr12:4429477-4430847	IMR90	lung:	n/a	n/a
26	TEAD4	chr12:4429583-4430881	ECC-1	luminal epithelium:	n/a	n/a
27	TAF1	chr12:4429707-4430757	A549	lung:	n/a	n/a
28	SP1	chr12:4429654-4430724	A549	lung:	n/a	chr12:4430227-4430240 chr12:4430186-4430207 chr12:4430230-4430242 chr12:4430161-4430170 chr12:4430640-4430654 chr12:4430261-4430270 chr12:4430260-4430272 chr12:4430230-4430242 chr12:4430232-4430241 chr12:4430159-4430171 chr12:4430159-4430171 chr12:4430231-4430240 chr12:4430262-4430271
29	MAX	chr12:4429653-4430666	MCF-7	breast:	n/a	n/a
30	POLR2A	chr12:4429594-4430976	Raji	blood:	n/a	n/a
31	MAX	chr12:4429465-4430748	ECC-1	luminal epithelium:	n/a	n/a
32	E2F6	chr12:4429706-4430842	H1-hESC	embryonic stem cell:	n/a	chr12:4430160-4430169 chr12:4430214-4430223
33	SP1	chr12:4429494-4430603	H1-hESC	embryonic stem cell:	n/a	chr12:4430227-4430240 chr12:4430186-4430207 chr12:4430230-4430242 chr12:4430161-4430170 chr12:4430261-4430270 chr12:4430260-4430272 chr12:4430230-4430242 chr12:4430232-4430241 chr12:4430159-4430171 chr12:4430159-4430171 chr12:4430231-4430240 chr12:4430262-4430271
34	RUNX3	chr12:4429560-4430842	GM12878	blood:	n/a	chr12:4430074-4430083 chr12:4430065-4430082
35	MTA3	chr12:4429356-4431016	GM12878	blood:	n/a	n/a
36	CHD2	chr12:4429697-4430537	H1-hESC	embryonic stem cell:	n/a	n/a
37	JUND	chr12:4429692-4430778	H1-hESC	embryonic stem cell:	n/a	chr12:4430189-4430198
38	POLR2A	chr12:4429689-4430766	SK-N-MC	brain:	n/a	n/a
39	RCOR1	chr12:4429492-4431232	IMR90	lung:	n/a	n/a
40	MAX	chr12:4429700-4430847	Hela-S3	cervix:	n/a	n/a
41	TCF12	chr12:4429675-4430789	ECC-1	luminal epithelium:	n/a	chr12:4430174-4430181 chr12:4430655-4430665
42	POLR2A	chr12:4429684-4430809	GM19099	blood:	n/a	n/a
43	POLR2A	chr12:4429579-4430936	GM12878	blood:	n/a	n/a
44	ARID3A	chr12:4429673-4430127	HepG2	liver:	n/a	n/a
45	MYC	chr12:4429636-4430490	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr12:4429469-4430916	GM12878	blood:	n/a	n/a
47	POLR2A	chr12:4429695-4430631	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr12:4429485-4430800	HUVEC	blood vessel:	n/a	n/a
49	GTF2F1	chr12:4429556-4430761	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr12:4429503-4430865	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:4426548..4433577-chr12:4433933..4442534,18	MCF-7	breast:
2	chr12:4423393..4425090-chr12:4428097..4430311,2	MCF-7	breast:
3	chr1:45196411..45196952-chr12:4429178..4430143,2	Hela-S3	cervix:
4	chr12:4429599..4431806-chr12:4431881..4434524,2	MCF-7	breast:

Variant related genes	Relation type
C12orf5	TF binding region
ENSG00000213970	Chromatin interaction
ENSG00000078237	Chromatin interaction
ENSG00000200169	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10774217	0.82[JPT][hapmap]
rs11063079	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv832317	chr12:4315298-4435615	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv468985	chr12:4423612-4473329	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv557122	chr12:4423612-4473329	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4413200-4429800	Weak transcription	Spleen	Spleen
2	chr12:4429400-4429800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:4429400-4429800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr12:4429400-4429800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr12:4429400-4429800	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr12:4429400-4429800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr12:4429400-4429800	Flanking Active TSS	Brain Hippocampus Middle	brain
8	chr12:4429400-4429800	Flanking Active TSS	Colon Smooth Muscle	Colon
9	chr12:4429400-4429800	Flanking Active TSS	Fetal Brain Female	brain
10	chr12:4429400-4429800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr12:4429400-4429800	Flanking Active TSS	A549	lung
12	chr12:4429400-4429800	Flanking Active TSS	NHEK	skin
13	chr12:4429400-4430000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr12:4429400-4430000	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr12:4429400-4430000	Flanking Active TSS	Primary B cells from peripheral blood	blood
16	chr12:4429400-4430000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr12:4429400-4430000	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr12:4429400-4430000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:4429400-4430000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr12:4429400-4430000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr12:4429400-4430000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:4429400-4430000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr12:4429400-4430000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:4429400-4430000	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr12:4429400-4430000	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr12:4429400-4430000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr12:4429400-4430000	Flanking Active TSS	Rectal Smooth Muscle	rectum
28	chr12:4429400-4430000	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr12:4429400-4430000	Flanking Active TSS	Dnd41	blood
30	chr12:4429400-4430000	Flanking Active TSS	Hela-S3	cervix
31	chr12:4429400-4430000	Flanking Active TSS	HUVEC	blood vessel
32	chr12:4429400-4430000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr12:4429400-4430000	Flanking Active TSS	Osteobl	bone
34	chr12:4429400-4430200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr12:4429400-4430600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:4429400-4430600	Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr12:4429400-4430800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:4429400-4431200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr12:4429400-4431200	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr12:4429400-4431200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:4429400-4431200	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr12:4429400-4431400	Active TSS	H1 Cell Line	embryonic stem cell
43	chr12:4429400-4431400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:4429400-4431400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:4429400-4431400	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr12:4429400-4431400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:4429400-4431400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:4429400-4431400	Active TSS	Brain Angular Gyrus	brain
49	chr12:4429400-4431400	Active TSS	Brain Anterior Caudate	brain
50	chr12:4429400-4431400	Active TSS	HMEC	breast

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