Variant report

Variant	rs7978407
Chromosome Location	chr12:31882208-31882209
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:520)
CpG islands
(count:122)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:520 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYA	chr12:31881815-31882241	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr12:31882120-31882270	RPTEC	kidney:	n/a	n/a
3	SIN3AK20	chr12:31881316-31882662	MCF-7	breast:	n/a	n/a
4	TCF7L2	chr12:31881608-31882673	PANC-1	pancreas:	n/a	n/a
5	SRF	chr12:31881935-31882240	HepG2	liver:	n/a	n/a
6	BCLAF1	chr12:31881213-31882608	GM12878	blood:	n/a	chr12:31882122-31882131 chr12:31882287-31882300 chr12:31881867-31881876 chr12:31882279-31882292
7	ELF1	chr12:31881644-31882482	MCF-7	breast:	n/a	chr12:31881960-31881973
8	JUND	chr12:31881875-31882668	H1-hESC	embryonic stem cell:	n/a	chr12:31881880-31881889 chr12:31882043-31882052
9	CREB1	chr12:31881321-31882680	GM12878	blood:	n/a	chr12:31882041-31882054
10	CTCF	chr12:31881746-31882328	GM12878	blood:	n/a	n/a
11	MBD4	chr12:31881858-31882405	HepG2	liver:	n/a	n/a
12	REST	chr12:31880987-31882899	H1-neurons	neurons:	n/a	chr12:31881881-31881894 chr12:31882831-31882849
13	ELK1	chr12:31881886-31882763	K562	blood:	n/a	n/a
14	E2F6	chr12:31881815-31882751	H1-hESC	embryonic stem cell:	n/a	chr12:31882044-31882053 chr12:31882042-31882051
15	POLR2A	chr12:31881120-31882552	PANC-1	pancreas:	n/a	n/a
16	CREB1	chr12:31881561-31882522	HepG2	liver:	n/a	chr12:31882041-31882054
17	TBP	chr12:31881612-31882456	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:31881251-31882534	GM15510	blood:	n/a	n/a
19	JUN	chr12:31881255-31883227	K562	blood:	n/a	chr12:31881799-31881808 chr12:31882039-31882052 chr12:31881880-31881889 chr12:31881800-31881809 chr12:31882043-31882052
20	TAF1	chr12:31881809-31882668	A549	lung:	n/a	n/a
21	CTCF	chr12:31882060-31882210	AG09309	skin:	n/a	n/a
22	STAT3	chr12:31881964-31882250	MCF10A-Er-Src	breast:	n/a	n/a
23	ELF1	chr12:31881619-31882496	SK-N-SH	brain:	n/a	chr12:31881960-31881973
24	EGR1	chr12:31881579-31882351	K562	blood:	n/a	chr12:31881799-31881809 chr12:31881800-31881813 chr12:31882192-31882216
25	BCLAF1	chr12:31882035-31884018	K562	blood:	n/a	chr12:31882122-31882131 chr12:31882287-31882300 chr12:31882279-31882292
26	TCF7L2	chr12:31881372-31882576	Hela-S3	cervix:	n/a	n/a
27	MXI1	chr12:31881261-31882266	H1-hESC	embryonic stem cell:	n/a	n/a
28	REST	chr12:31882062-31882387	PANC-1	pancreas:	n/a	n/a
29	USF1	chr12:31881833-31882390	SK-N-SH	brain:	n/a	n/a
30	TBP	chr12:31881244-31882665	GM12878	blood:	n/a	n/a
31	SIX5	chr12:31881876-31882412	K562	blood:	n/a	chr12:31882204-31882213 chr12:31882206-31882215
32	ARID3A	chr12:31881277-31882558	HepG2	liver:	n/a	n/a
33	TAF1	chr12:31881561-31882309	Hela-S3	cervix:	n/a	n/a
34	E2F6	chr12:31881226-31882986	A549	lung:	n/a	chr12:31882044-31882053 chr12:31882042-31882051
35	POLR2A	chr12:31881803-31882457	HepG2	liver:	n/a	n/a
36	MAX	chr12:31881266-31882656	HepG2	liver:	n/a	n/a
37	EP300	chr12:31881879-31882389	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr12:31881547-31882536	A549	lung:	n/a	n/a
39	POLR2A	chr12:31881294-31882605	H1-neurons	neurons:	n/a	n/a
40	MAFK	chr12:31881310-31883016	K562	blood:	n/a	n/a
41	ZC3H11A	chr12:31881924-31882492	K562	blood:	n/a	n/a
42	POLR2A	chr12:31881140-31882671	GM12892	blood:	n/a	n/a
43	BRCA1	chr12:31881250-31882454	Hela-S3	cervix:	n/a	n/a
44	CTCF	chr12:31882100-31882250	GM12865	blood:	n/a	n/a
45	ELK4	chr12:31881876-31882335	Hela-S3	cervix:	n/a	n/a
46	MYC	chr12:31880923-31883371	K562	blood:	n/a	n/a
47	NRF1	chr12:31881563-31882539	GM12878	blood:	n/a	n/a
48	TAF1	chr12:31881487-31882441	K562	blood:	n/a	n/a
49	YY1	chr12:31881438-31882498	HepG2	liver:	n/a	chr12:31882274-31882288 chr12:31881799-31881808
50	POLR2A	chr12:31881283-31882558	GM12891	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:31882198-31882248	HRPEpiC	eye:	n/a
2	chr12:31882198-31882248	H1-hESC	embryonic stem cell:	embryo
3	chr12:31882203-31882253	H1-hESC	embryonic stem cell:	embryo
4	chr12:31882198-31882248	HMEC	breast:	n/a
5	chr12:31882203-31882253	ProgFib	skin:	n/a
6	chr12:31882198-31882248	HIPEpiC	eye:	n/a
7	chr12:31882203-31882253	HRE	kidney:	n/a
8	chr12:31882203-31882253	NHBE	bronchial:	n/a
9	chr12:31882198-31882248	T-47D	breast:	n/a
10	chr12:31882198-31882248	AoSMC	blood vessel:	n/a
11	chr12:31882198-31882248	GM19239	blood:	n/a
12	chr12:31882203-31882253	HEEpiC	esophagus:	n/a
13	chr12:31882203-31882253	NB4	blood:	n/a
14	chr12:31882203-31882253	HMEC	breast:	n/a
15	chr12:31882198-31882248	SK-N-SH_RA	brain:	n/a
16	chr12:31882198-31882248	HL-60	blood:	n/a
17	chr12:31882198-31882248	HUVEC	blood vessel:	n/a
18	chr12:31882198-31882248	ovcar-3	ovarian:	n/a
19	chr12:31882198-31882248	SKMC	muscle:	n/a
20	chr12:31882203-31882253	NH-A	brain:	n/a
21	chr12:31882198-31882248	NHBE	bronchial:	n/a
22	chr12:31882203-31882253	AG09319	gingival:	n/a
23	chr12:31882203-31882253	GM12892	blood:	n/a
24	chr12:31882198-31882248	AG04449	skin:	fetal
25	chr12:31882198-31882248	SK-N-SH	brain:	n/a
26	chr12:31882198-31882248	BJ	skin:	n/a
27	chr12:31882198-31882248	A549	lung:	n/a
28	chr12:31882198-31882248	NT2-D1	testis:	n/a
29	chr12:31882203-31882253	Caco-2	colon:	n/a
30	chr12:31882203-31882253	HCT-116	colon:	n/a
31	chr12:31882198-31882248	SAEC	small airway:	n/a
32	chr12:31882198-31882248	Hela-S3	cervix:	n/a
33	chr12:31882203-31882253	SK-N-SH_RA	brain:	n/a
34	chr12:31882203-31882253	HIPEpiC	eye:	n/a
35	chr12:31882203-31882253	AG09309	skin:	n/a
36	chr12:31882203-31882253	HEK293	kidney:	embryo
37	chr12:31882198-31882248	AG10803	skin:	n/a
38	chr12:31882198-31882248	AG09319	gingival:	n/a
39	chr12:31882198-31882248	NHDF-neo	bronchial:	n/a
40	chr12:31882203-31882253	HRPEpiC	eye:	n/a
41	chr12:31882203-31882253	MCF-7	breast:	n/a
42	chr12:31882198-31882248	HRCEpiC	kidney:	n/a
43	chr12:31882203-31882253	BJ	skin:	n/a
44	chr12:31882198-31882248	LNCaP	prostate:	n/a
45	chr12:31882203-31882253	U87	brain:	n/a
46	chr12:31882198-31882248	CMK	blood:	n/a
47	chr12:31882198-31882248	NH-A	brain:	n/a
48	chr12:31882203-31882253	PFSK-1	brain:	n/a
49	chr12:31882198-31882248	HCM	heart:	n/a
50	chr12:31882203-31882253	HRCEpiC	kidney:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:31880642..31885296-chr12:32110658..32113618,5	K562	blood:
2	chr12:31881243..31883910-chr12:32111522..32113326,3	MCF-7	breast:
3	chr12:31882162..31882742-chr8:125551065..125551799,2	Hela-S3	cervix:
4	chr12:31880708..31883036-chr12:32258362..32261321,3	K562	blood:
5	chr12:31880350..31888706-chr12:31898122..31903847,15	K562	blood:
6	chr12:31880235..31884620-chr12:31906466..31910642,5	K562	blood:
7	chr12:31477256..31480149-chr12:31881924..31883474,2	K562	blood:
8	chr12:31882068..31882792-chr14:75593054..75593701,2	Hela-S3	cervix:
9	chr12:31477256..31479632-chr12:31880019..31883424,4	K562	blood:

No data

Variant related genes	Relation type
AMN1	TF binding region
AMN1	CpG island
ENSG00000223722	Chromatin interaction
ENSG00000139146	Chromatin interaction
ENSG00000147684	Chromatin interaction
ENSG00000174718	Chromatin interaction
ENSG00000257530	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000151746	Chromatin interaction
ENSG00000119638	Chromatin interaction
ENSG00000256843	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10844000	0.81[AMR][1000 genomes]
rs10844003	0.82[AMR][1000 genomes]
rs11051525	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11051541	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11051545	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11051555	0.82[AMR][1000 genomes]
rs12813042	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12813399	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35517071	0.93[AMR][1000 genomes]
rs7134951	0.86[AMR][1000 genomes]
rs7297921	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7300260	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7302229	0.90[AMR][1000 genomes]
rs7953551	0.82[AMR][1000 genomes]
rs7960893	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7969019	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers 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 target site	41 gene(s)	inside rSNPs	diseases
4	esv3432694	chr12:31801467-32109828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv898966	chr12:31810126-31944985	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv898967	chr12:31858031-31899475	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv2422415	chr12:31863360-31930722	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv558100	chr12:31866833-32185924	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv1045464	chr12:31869888-32183792	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv541447	chr12:31869888-32183792	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	esv3363806	chr12:31872264-32410283	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
12	esv3508621	chr12:31872654-32410593	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
13	esv3508622	chr12:31872654-32410593	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
14	nsv558101	chr12:31876666-32006563	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
15	nsv1050448	chr12:31877289-31927006	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 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	chr12:31880600-31882800	Active TSS	K562	blood
2	chr12:31880800-31882400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr12:31880800-31882400	Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr12:31880800-31882400	Active TSS	Stomach Smooth Muscle	stomach
5	chr12:31880800-31882600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:31880800-31882600	Active TSS	Brain Anterior Caudate	brain
7	chr12:31880800-31882800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:31880800-31883000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr12:31881000-31882400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr12:31881000-31882400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:31881000-31882400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:31881000-31882400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:31881000-31882400	Active TSS	Brain Germinal Matrix	brain
14	chr12:31881000-31882400	Active TSS	Fetal Kidney	kidney
15	chr12:31881000-31882400	Active TSS	NH-A	brain
16	chr12:31881000-31882600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:31881000-31882600	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr12:31881000-31882600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:31881000-31882600	Active TSS	Brain Angular Gyrus	brain
20	chr12:31881000-31882600	Active TSS	Brain Cingulate Gyrus	brain
21	chr12:31881000-31882600	Active TSS	Fetal Brain Female	brain
22	chr12:31881000-31882600	Active TSS	Fetal Intestine Large	intestine
23	chr12:31881000-31882600	Active TSS	Fetal Intestine Small	intestine
24	chr12:31881000-31882800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:31881000-31882800	Active TSS	Colonic Mucosa	Colon
26	chr12:31881000-31882800	Active TSS	Right Ventricle	heart
27	chr12:31881000-31883000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:31881000-31883000	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr12:31881000-31883000	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr12:31881000-31883000	Active TSS	Psoas Muscle	Psoas
31	chr12:31881000-31883200	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr12:31881000-31883200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:31881000-31883200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:31881200-31882400	Active TSS	H1 Cell Line	embryonic stem cell
35	chr12:31881200-31882400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:31881200-31882400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:31881200-31882400	Active TSS	Primary T cells from cord blood	blood
38	chr12:31881200-31882400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:31881200-31882400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:31881200-31882600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:31881200-31882600	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr12:31881200-31882600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr12:31881200-31882600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:31881200-31882600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:31881200-31882600	Active TSS	Brain Substantia Nigra	brain
46	chr12:31881200-31882600	Active TSS	Colon Smooth Muscle	Colon
47	chr12:31881200-31882600	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr12:31881200-31882600	Active TSS	Placenta Amnion	Placenta Amnion
49	chr12:31881200-31882600	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr12:31881200-31882600	Active TSS	Thymus	Thymus

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