Variant report

Variant	rs1169287
Chromosome Location	chr12:121418356-121418357
allele	A/G
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	REST	chr12:121417773-121418503	ECC-1	luminal epithelium:	n/a	chr12:121418415-121418428 chr12:121418147-121418156 chr12:121418148-121418162 chr12:121418142-121418162 chr12:121418142-121418162
2	HEY1	chr12:121415737-121419289	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:121418102-121418423	A549	lung:	n/a	n/a
4	TEAD4	chr12:121417881-121418423	HepG2	liver:	n/a	n/a
5	FOXA1	chr12:121418030-121418376	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:121415550-121419599	HepG2	liver:	n/a	n/a
7	REST	chr12:121417779-121418484	ECC-1	luminal epithelium:	n/a	chr12:121418415-121418428 chr12:121418147-121418156 chr12:121418148-121418162 chr12:121418142-121418162 chr12:121418142-121418162
8	SP1	chr12:121417828-121419896	A549	lung:	n/a	chr12:121418655-121418664 chr12:121418414-121418428 chr12:121418308-121418317 chr12:121418127-121418134 chr12:121418964-121418976 chr12:121419279-121419293 chr12:121418966-121418975 chr12:121418654-121418666 chr12:121418307-121418316 chr12:121418965-121418974 chr12:121418420-121418434 chr12:121418654-121418666 chr12:121418656-121418665 chr12:121418961-121418975 chr12:121418358-121418370 chr12:121418235-121418249 chr12:121418655-121418665 chr12:121418719-121418733 chr12:121418964-121418976 chr12:121418651-121418665 chr12:121418360-121418369
9	REST	chr12:121417868-121418404	PFSK-1	brain:	n/a	chr12:121418147-121418156 chr12:121418148-121418162 chr12:121418142-121418162 chr12:121418142-121418162
10	POLR2A	chr12:121418083-121418756	A549	lung:	n/a	n/a
11	POLR2A	chr12:121415325-121419806	HepG2	liver:	n/a	n/a
12	ZNF143	chr12:121417975-121418363	H1-hESC	embryonic stem cell:	n/a	n/a
13	HNF4G	chr12:121417957-121418711	HepG2	liver:	n/a	chr12:121418537-121418552 chr12:121418538-121418550 chr12:121418535-121418547 chr12:121418537-121418552 chr12:121418538-121418550 chr12:121418537-121418552 chr12:121418537-121418552 chr12:121418284-121418296
14	REST	chr12:121417913-121418408	MCF-7	breast:	n/a	chr12:121418147-121418156 chr12:121418148-121418162 chr12:121418142-121418162 chr12:121418142-121418162
15	REST	chr12:121417738-121418687	A549	lung:	n/a	chr12:121418415-121418428 chr12:121418147-121418156 chr12:121418148-121418162 chr12:121418142-121418162 chr12:121418142-121418162
16	JUND	chr12:121417970-121418430	A549	lung:	n/a	chr12:121418094-121418106
17	FOXA2	chr12:121418024-121418436	A549	lung:	n/a	n/a
18	TCF12	chr12:121417813-121418394	A549	lung:	n/a	n/a
19	RAD21	chr12:121418003-121418381	HepG2	liver:	n/a	chr12:121418073-121418087 chr12:121418065-121418078 chr12:121418072-121418091 chr12:121418074-121418088
20	REST	chr12:121417872-121418373	U87	brain:	n/a	chr12:121418147-121418156 chr12:121418148-121418162 chr12:121418142-121418162 chr12:121418142-121418162
21	TCF12	chr12:121417737-121419987	A549	lung:	n/a	n/a
22	HNF4A	chr12:121417990-121418403	HepG2	liver:	n/a	chr12:121418284-121418296
23	REST	chr12:121417907-121418413	H1-hESC	embryonic stem cell:	n/a	chr12:121418147-121418156 chr12:121418148-121418162 chr12:121418142-121418162 chr12:121418142-121418162
24	NR3C1	chr12:121417993-121418489	A549	lung:	n/a	chr12:121418230-121418243
25	NFIC	chr12:121417797-121418389	HepG2	liver:	n/a	n/a
26	SIN3AK20	chr12:121417967-121418433	HepG2	liver:	n/a	n/a
27	EP300	chr12:121417762-121419990	A549	lung:	n/a	chr12:121417810-121417826
28	REST	chr12:121417792-121418475	PANC-1	pancreas:	n/a	chr12:121418415-121418428 chr12:121418147-121418156 chr12:121418148-121418162 chr12:121418142-121418162 chr12:121418142-121418162
29	HDAC2	chr12:121417920-121418504	HepG2	liver:	n/a	chr12:121418142-121418161
30	CHD2	chr12:121417988-121418495	HepG2	liver:	n/a	n/a
31	HNF4G	chr12:121417891-121418521	HepG2	liver:	n/a	chr12:121418284-121418296
32	CEBPD	chr12:121417895-121418448	HepG2	liver:	n/a	n/a
33	TCF12	chr12:121417941-121418372	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr12:121417754-121418838	HepG2	liver:	n/a	n/a
35	TAF1	chr12:121417922-121418859	HepG2	liver:	n/a	n/a
36	POLR2A	chr12:121417926-121418792	HepG2	liver:	n/a	n/a
37	JUND	chr12:121418020-121418393	HepG2	liver:	n/a	chr12:121418094-121418106
38	HDAC2	chr12:121417994-121418469	HepG2	liver:	n/a	chr12:121418142-121418161
39	EP300	chr12:121418037-121418471	HepG2	liver:	n/a	n/a
40	FOXA2	chr12:121417957-121419962	A549	lung:	n/a	n/a
41	ZBTB7A	chr12:121418106-121418526	HepG2	liver:	n/a	chr12:121418257-121418265
42	MAX	chr12:121415630-121419965	A549	lung:	n/a	chr12:121416508-121416515 chr12:121416545-121416554 chr12:121418418-121418428 chr12:121416195-121416205
43	HNF4A	chr12:121417979-121418628	HepG2	liver:	n/a	chr12:121418537-121418552 chr12:121418538-121418550 chr12:121418535-121418547 chr12:121418537-121418552 chr12:121418538-121418550 chr12:121418537-121418552 chr12:121418537-121418552 chr12:121418284-121418296
44	NFIC	chr12:121417772-121418399	HepG2	liver:	n/a	n/a
45	TAF1	chr12:121417966-121418463	HepG2	liver:	n/a	n/a
46	REST	chr12:121416814-121419966	A549	lung:	n/a	chr12:121417024-121417033 chr12:121418415-121418428 chr12:121418147-121418156 chr12:121417597-121417617 chr12:121416921-121416934 chr12:121418828-121418836 chr12:121418148-121418162 chr12:121418142-121418162 chr12:121418142-121418162 chr12:121416912-121416925
47	MBD4	chr12:121417780-121418458	HepG2	liver:	n/a	n/a
48	TCF12	chr12:121418048-121418358	HepG2	liver:	n/a	n/a
49	MAZ	chr12:121417993-121418705	HepG2	liver:	n/a	chr12:121418418-121418428
50	SP1	chr12:121417899-121419116	HepG2	liver:	n/a	chr12:121418655-121418664 chr12:121418414-121418428 chr12:121418308-121418317 chr12:121418127-121418134 chr12:121418964-121418976 chr12:121418966-121418975 chr12:121418654-121418666 chr12:121418307-121418316 chr12:121418965-121418974 chr12:121418420-121418434 chr12:121418654-121418666 chr12:121418656-121418665 chr12:121418961-121418975 chr12:121418358-121418370 chr12:121418235-121418249 chr12:121418655-121418665 chr12:121418719-121418733 chr12:121418964-121418976 chr12:121418651-121418665 chr12:121418360-121418369

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121410040..121412493-chr12:121417620..121420402,3	MCF-7	breast:

Variant related genes	Relation type
HNF1A-AS1	TF binding region
ENSG00000272214	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1169285	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1169293	1.00[YRI][hapmap]
rs1169295	0.84[AFR][1000 genomes]
rs2245407	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs3751152	1.00[CEU][hapmap]
rs55783344	0.82[EUR][1000 genomes]
rs56087915	0.88[EUR][1000 genomes]
rs56357256	0.94[EUR][1000 genomes]
rs56382736	1.00[EUR][1000 genomes]
rs58498324	0.94[EUR][1000 genomes]
rs657647	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv899561	chr12:121376416-121525591	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	esv3357747	chr12:121405281-121427388	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1037195	chr12:121408540-121470375	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121409600-121418400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:121409600-121422200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:121410000-121418600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:121414600-121418800	Active TSS	Gastric	stomach
5	chr12:121414600-121419000	Weak transcription	Fetal Lung	lung
6	chr12:121415400-121418800	Active TSS	Rectal Smooth Muscle	rectum
7	chr12:121415400-121419200	Active TSS	Fetal Kidney	kidney
8	chr12:121415400-121419800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:121415600-121418600	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr12:121416000-121418800	Active TSS	Sigmoid Colon	Sigmoid Colon
11	chr12:121416000-121418800	Active TSS	Small Intestine	intestine
12	chr12:121416000-121419000	Active TSS	Fetal Intestine Large	intestine
13	chr12:121416000-121419000	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr12:121416000-121419200	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr12:121416200-121418400	Active TSS	Liver	Liver
16	chr12:121416200-121418800	Active TSS	Pancreas	Pancrea
17	chr12:121416200-121419000	Active TSS	Colonic Mucosa	Colon
18	chr12:121416200-121419000	Active TSS	Duodenum Mucosa	Duodenum
19	chr12:121416200-121419000	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr12:121416200-121419000	Active TSS	Stomach Mucosa	stomach
21	chr12:121417400-121418800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:121417400-121418800	Active TSS	Fetal Stomach	stomach
23	chr12:121417600-121419000	Active TSS	Fetal Intestine Small	intestine
24	chr12:121417800-121419600	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr12:121418000-121418600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:121418000-121418800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr12:121418000-121419000	Active TSS	HepG2	liver
28	chr12:121418000-121420000	Flanking Active TSS	A549	lung
29	chr12:121418200-121418600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:121418200-121418600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:121418200-121418800	Enhancers	H1 Cell Line	embryonic stem cell
32	chr12:121418200-121418800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:121418200-121419000	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr12:121418200-121419200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:121418200-121421800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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