Variant report

Variant	rs12088109
Chromosome Location	chr1:168465025-168465026
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	CTCF	chr1:168464974-168465066	Kidney_OC	kidney:	n/a	n/a
2	MYBL2	chr1:168464638-168465304	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:168464719-168465219	HepG2	liver:	n/a	n/a
4	HNF4A	chr1:168464852-168465118	HepG2	liver:	n/a	chr1:168464980-168464995
5	RXRA	chr1:168464761-168465133	HepG2	liver:	n/a	chr1:168465009-168465018
6	EP300	chr1:168464746-168465270	HepG2	liver:	n/a	n/a
7	HEY1	chr1:168464769-168465157	HepG2	liver:	n/a	n/a
8	FOXA1	chr1:168464673-168465247	HepG2	liver:	n/a	n/a
9	HNF4A	chr1:168464782-168465117	HepG2	liver:	n/a	chr1:168464980-168464995
10	NFIC	chr1:168464622-168465224	HepG2	liver:	n/a	n/a
11	MBD4	chr1:168464687-168465206	HepG2	liver:	n/a	n/a
12	JUN	chr1:168465013-168465437	HepG2	liver:	n/a	chr1:168465135-168465144 chr1:168465323-168465336
13	IKZF1	chr1:168464807-168465038	GM12878	blood:	n/a	n/a
14	HEY1	chr1:168464635-168465233	HepG2	liver:	n/a	n/a
15	EP300	chr1:168464685-168465142	HepG2	liver:	n/a	n/a
16	FOXA1	chr1:168464676-168465238	HepG2	liver:	n/a	n/a
17	TEAD4	chr1:168464726-168465282	HepG2	liver:	n/a	n/a
18	FOXA2	chr1:168464756-168465161	HepG2	liver:	n/a	n/a
19	FOXA1	chr1:168464645-168465245	HepG2	liver:	n/a	n/a
20	SP1	chr1:168464660-168465192	HepG2	liver:	n/a	n/a
21	MAX	chr1:168464622-168465321	HepG2	liver:	n/a	n/a
22	TBP	chr1:168464829-168465108	HepG2	liver:	n/a	n/a
23	MYBL2	chr1:168464716-168465212	HepG2	liver:	n/a	n/a
24	ARID3A	chr1:168464753-168465207	HepG2	liver:	n/a	n/a
25	POLR2A	chr1:168464643-168465070	HepG2	liver:	n/a	n/a
26	REST	chr1:168464717-168465102	HepG2	liver:	n/a	n/a
27	FOXA2	chr1:168464459-168465399	HepG2	liver:	n/a	n/a
28	ELF1	chr1:168464806-168465103	HepG2	liver:	n/a	n/a
29	FOXA1	chr1:168464684-168465232	HepG2	liver:	n/a	n/a
30	RAD21	chr1:168464831-168465145	HepG2	liver:	n/a	n/a
31	HNF4G	chr1:168464753-168465123	HepG2	liver:	n/a	n/a
32	MBD4	chr1:168464706-168465105	HepG2	liver:	n/a	n/a
33	HNF4A	chr1:168464821-168465161	HepG2	liver:	n/a	chr1:168464980-168464995
34	FOXA2	chr1:168464822-168465176	A549	lung:	n/a	n/a
35	NFIC	chr1:168464721-168465219	HepG2	liver:	n/a	n/a
36	POLR2A	chr1:168464890-168465129	HepG2	liver:	n/a	n/a
37	POLR2A	chr1:168464714-168465111	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000237658	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10918889	1.00[EUR][1000 genomes]
rs10918890	1.00[EUR][1000 genomes]
rs10918891	1.00[EUR][1000 genomes]
rs10918892	1.00[EUR][1000 genomes]
rs10918893	1.00[EUR][1000 genomes]
rs10918895	1.00[EUR][1000 genomes]
rs10918896	1.00[EUR][1000 genomes]
rs10918913	1.00[EUR][1000 genomes]
rs10918914	1.00[EUR][1000 genomes]
rs10918915	1.00[EUR][1000 genomes]
rs10918916	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10918918	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10918929	1.00[EUR][1000 genomes]
rs12058640	1.00[EUR][1000 genomes]
rs12059095	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12059526	1.00[EUR][1000 genomes]
rs12059722	1.00[EUR][1000 genomes]
rs12060094	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12060180	1.00[EUR][1000 genomes]
rs12061311	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12061688	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12062599	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12064517	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12064716	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12065600	1.00[EUR][1000 genomes]
rs12069600	1.00[EUR][1000 genomes]
rs12071398	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12071533	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12071580	1.00[EUR][1000 genomes]
rs12071946	1.00[EUR][1000 genomes]
rs12072708	1.00[EUR][1000 genomes]
rs12072756	1.00[EUR][1000 genomes]
rs12073928	1.00[EUR][1000 genomes]
rs12075383	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12076618	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12078253	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080560	1.00[EUR][1000 genomes]
rs12086182	1.00[EUR][1000 genomes]
rs12087491	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12088031	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12093369	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12093899	1.00[EUR][1000 genomes]
rs12095242	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12095394	1.00[EUR][1000 genomes]
rs12096533	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12096552	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12563551	1.00[EUR][1000 genomes]
rs1323524	1.00[EUR][1000 genomes]
rs16860744	1.00[EUR][1000 genomes]
rs16860745	1.00[EUR][1000 genomes]
rs16860750	1.00[EUR][1000 genomes]
rs16860759	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2092400	1.00[EUR][1000 genomes]
rs28537856	1.00[AMR][1000 genomes]
rs58887669	1.00[EUR][1000 genomes]
rs60094342	1.00[EUR][1000 genomes]
rs6674956	1.00[EUR][1000 genomes]
rs73027529	1.00[EUR][1000 genomes]
rs73031504	1.00[EUR][1000 genomes]
rs73031508	1.00[EUR][1000 genomes]
rs74120912	1.00[EUR][1000 genomes]
rs74120961	1.00[EUR][1000 genomes]
rs74120963	1.00[EUR][1000 genomes]
rs74120965	1.00[EUR][1000 genomes]
rs74123943	1.00[EUR][1000 genomes]
rs74123944	1.00[EUR][1000 genomes]
rs7526174	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014626	chr1:168441288-168642731	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535196	chr1:168441288-168642731	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1011821	chr1:168441488-168642592	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv535197	chr1:168441488-168642592	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1008852	chr1:168449940-168643905	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv535198	chr1:168449940-168643905	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1007846	chr1:168449940-168687265	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168454600-168475200	Weak transcription	Small Intestine	intestine
2	chr1:168455000-168466800	Weak transcription	Ovary	ovary
3	chr1:168455000-168466800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:168457600-168467200	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:168457800-168468600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:168461200-168466800	Weak transcription	Stomach Mucosa	stomach
7	chr1:168461400-168466600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:168461400-168466800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:168461400-168466800	Weak transcription	Fetal Stomach	stomach
10	chr1:168461400-168467000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:168461600-168466400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:168461600-168466600	Weak transcription	Fetal Lung	lung
13	chr1:168462000-168467000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:168462000-168473400	Weak transcription	Pancreas	Pancrea
15	chr1:168462200-168466400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:168462800-168473600	Weak transcription	Psoas Muscle	Psoas
17	chr1:168464000-168465200	Enhancers	Rectal Smooth Muscle	rectum
18	chr1:168464400-168469800	Enhancers	Fetal Intestine Large	intestine
19	chr1:168464400-168469800	Enhancers	Fetal Intestine Small	intestine
20	chr1:168464600-168465200	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr1:168464800-168465200	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr1:168464800-168465200	Active TSS	A549	lung
23	chr1:168464800-168467000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:168465000-168465400	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:168465000-168465400	Flanking Active TSS	HepG2	liver
26	chr1:168465000-168465800	Enhancers	Liver	Liver
27	chr1:168465000-168465800	Enhancers	Duodenum Mucosa	Duodenum

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