Variant report

Variant	rs1879399
Chromosome Location	chr12:31524173-31524174
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	TAF7	chr12:31523802-31524404	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF263	chr12:31522544-31524392	HEK293-T-REx	kidney:	n/a	chr12:31523877-31523886
3	HEY1	chr12:31523657-31524210	HepG2	liver:	n/a	n/a
4	TEAD4	chr12:31523643-31524473	HepG2	liver:	n/a	n/a
5	TAF1	chr12:31523511-31524308	H1-hESC	embryonic stem cell:	n/a	n/a
6	SIN3A	chr12:31523564-31524441	H1-hESC	embryonic stem cell:	n/a	n/a
7	HEY1	chr12:31523612-31524175	HepG2	liver:	n/a	n/a
8	CHD1	chr12:31521706-31524671	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr12:31523156-31524264	HepG2	liver:	n/a	n/a
10	BHLHE40	chr12:31523424-31524225	K562	blood:	n/a	n/a
11	TBP	chr12:31523488-31524563	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr12:31522641-31524622	H1-hESC	embryonic stem cell:	n/a	n/a
13	TAF1	chr12:31523770-31524266	H1-hESC	embryonic stem cell:	n/a	n/a
14	CEBPB	chr12:31523475-31524255	H1-hESC	embryonic stem cell:	n/a	n/a
15	NR2F2	chr12:31523623-31524248	HepG2	liver:	n/a	n/a
16	JUND	chr12:31522733-31524476	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr12:31523667-31524232	H1-hESC	embryonic stem cell:	n/a	n/a
18	TEAD4	chr12:31523758-31524477	H1-hESC	embryonic stem cell:	n/a	n/a
19	ARID3A	chr12:31523752-31524257	HepG2	liver:	n/a	n/a
20	CHD2	chr12:31523037-31524401	H1-hESC	embryonic stem cell:	n/a	n/a
21	TBP	chr12:31523796-31524463	HepG2	liver:	n/a	n/a
22	BACH1	chr12:31523808-31524448	H1-hESC	embryonic stem cell:	n/a	n/a
23	HDAC2	chr12:31523789-31524341	HepG2	liver:	n/a	n/a
24	POLR2A	chr12:31523706-31524465	H1-hESC	embryonic stem cell:	n/a	n/a
25	SP1	chr12:31523495-31524559	H1-hESC	embryonic stem cell:	n/a	chr12:31523882-31523896
26	KAP1	chr12:31522644-31524373	HEK293	kidney:	n/a	n/a
27	HNF4A	chr12:31523791-31524193	HepG2	liver:	n/a	chr12:31524031-31524046 chr12:31523918-31523932 chr12:31524032-31524045 chr12:31523919-31523931 chr12:31524033-31524045 chr12:31524031-31524046 chr12:31524031-31524046
28	POLR2A	chr12:31521505-31524812	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr12:31523130-31524383	H1-hESC	embryonic stem cell:	n/a	n/a
30	YY1	chr12:31523618-31524196	H1-hESC	embryonic stem cell:	n/a	n/a
31	HNF4G	chr12:31523798-31524311	HepG2	liver:	n/a	chr12:31524031-31524046 chr12:31524032-31524047 chr12:31523918-31523932 chr12:31524032-31524045 chr12:31523919-31523931 chr12:31524033-31524045 chr12:31524031-31524046
32	POLR2A	chr12:31523571-31524251	H1-hESC	embryonic stem cell:	n/a	n/a
33	KAP1	chr12:31521482-31524528	U2OS	brain:	n/a	n/a
34	MAX	chr12:31523634-31524231	H1-hESC	embryonic stem cell:	n/a	n/a
35	HNF4A	chr12:31523835-31524217	HepG2	liver:	n/a	chr12:31524031-31524046 chr12:31523918-31523932 chr12:31524032-31524045 chr12:31523919-31523931 chr12:31524033-31524045 chr12:31524031-31524046 chr12:31524031-31524046
36	TCF7L2	chr12:31523104-31524278	HEK293	kidney:	n/a	n/a
37	RAD21	chr12:31523730-31524501	H1-hESC	embryonic stem cell:	n/a	n/a
38	NFIC	chr12:31523684-31524186	HepG2	liver:	n/a	n/a
39	SP4	chr12:31523765-31524483	H1-hESC	embryonic stem cell:	n/a	n/a
40	JUND	chr12:31523851-31524184	HepG2	liver:	n/a	n/a
41	ATF2	chr12:31523591-31524486	H1-hESC	embryonic stem cell:	n/a	n/a
42	SP1	chr12:31523602-31524561	H1-hESC	embryonic stem cell:	n/a	chr12:31523882-31523896
43	MYC	chr12:31523781-31524225	H1-hESC	embryonic stem cell:	n/a	n/a
44	ATF2	chr12:31522886-31524307	H1-hESC	embryonic stem cell:	n/a	n/a
45	CREB1	chr12:31523523-31524443	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31477279..31478888-chr12:31523877..31525734,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256232	TF binding region
ENSG00000139146	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12812075	1.00[ASN][1000 genomes]
rs12812141	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816170	1.00[ASN][1000 genomes]
rs12816386	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821808	1.00[ASN][1000 genomes]
rs12822601	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12831480	1.00[ASN][1000 genomes]
rs1879398	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34007930	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34184789	1.00[ASN][1000 genomes]
rs34308937	0.81[EUR][1000 genomes]
rs34450466	1.00[ASN][1000 genomes]
rs34585237	1.00[ASN][1000 genomes]
rs34642866	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34949976	1.00[ASN][1000 genomes]
rs34955459	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35029695	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35692484	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931485	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931498	1.00[ASN][1000 genomes]
rs4931503	1.00[ASN][1000 genomes]
rs4931504	1.00[ASN][1000 genomes]
rs55771933	1.00[ASN][1000 genomes]
rs56183451	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56234529	1.00[ASN][1000 genomes]
rs56327034	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66479670	1.00[ASN][1000 genomes]
rs66520413	1.00[ASN][1000 genomes]
rs66552209	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66635949	1.00[ASN][1000 genomes]
rs67963293	1.00[ASN][1000 genomes]
rs68030436	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455661	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71455668	1.00[ASN][1000 genomes]
rs71455669	1.00[ASN][1000 genomes]
rs73080503	1.00[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	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv832364	chr12:31467990-31648144	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription 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	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31521200-31524600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:31521600-31524200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:31521600-31524400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:31521600-31524400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:31521600-31524400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr12:31521600-31524400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr12:31521600-31524400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr12:31521600-31524400	Flanking Active TSS	HepG2	liver
9	chr12:31521600-31524600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr12:31521600-31524800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:31522200-31524200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr12:31522200-31524600	Enhancers	A549	lung
13	chr12:31522400-31524400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:31522400-31524600	Flanking Active TSS	Fetal Intestine Small	intestine
15	chr12:31522600-31524200	Flanking Active TSS	Fetal Kidney	kidney
16	chr12:31522600-31524400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
17	chr12:31522600-31524400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:31522600-31524400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr12:31522600-31524800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr12:31522800-31524200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
21	chr12:31522800-31524200	Active TSS	Rectal Smooth Muscle	rectum
22	chr12:31522800-31524400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr12:31522800-31524400	Flanking Active TSS	Fetal Intestine Large	intestine
24	chr12:31523000-31524400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:31523000-31524400	Enhancers	Brain Germinal Matrix	brain
26	chr12:31523000-31524600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr12:31523200-31524200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr12:31523200-31524200	Enhancers	NH-A	brain
29	chr12:31523200-31524400	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr12:31523200-31524600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr12:31523400-31524400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr12:31523400-31524600	Enhancers	Placenta	Placenta
33	chr12:31523400-31524600	Enhancers	HUVEC	blood vessel
34	chr12:31523400-31537600	Weak transcription	Fetal Brain Female	brain
35	chr12:31523600-31524200	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr12:31523600-31524200	Enhancers	Fetal Muscle Leg	muscle
37	chr12:31523600-31524400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:31523600-31524400	Enhancers	Brain Substantia Nigra	brain
39	chr12:31523600-31524400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr12:31523600-31524400	Enhancers	Fetal Heart	heart
41	chr12:31523600-31524400	Enhancers	Fetal Lung	lung
42	chr12:31523600-31524600	Active TSS	H9 Cell Line	embryonic stem cell
43	chr12:31523600-31524600	Enhancers	Placenta Amnion	Placenta Amnion
44	chr12:31523800-31524200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:31523800-31524200	Enhancers	Stomach Mucosa	stomach
46	chr12:31523800-31524200	Enhancers	Osteobl	bone
47	chr12:31523800-31524400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:31523800-31524400	Enhancers	Brain Hippocampus Middle	brain
49	chr12:31523800-31524400	Enhancers	Ovary	ovary
50	chr12:31523800-31524400	Enhancers	Skeletal Muscle Male	skeletal muscle

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