Variant report

Variant	rs12652934
Chromosome Location	chr5:179231248-179231249
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr5:179230599-179231349	NB4	blood:	n/a	chr5:179231289-179231305 chr5:179231022-179231032
2	POLR2A	chr5:179228800-179231391	K562	blood:	n/a	n/a
3	POLR2A	chr5:179229963-179231387	GM12892	blood:	n/a	n/a
4	POLR2A	chr5:179230816-179231348	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr5:179230596-179231464	K562	blood:	n/a	n/a
6	POLR2A	chr5:179230773-179231282	HepG2	liver:	n/a	n/a
7	MAX	chr5:179230548-179231411	NB4	blood:	n/a	chr5:179231289-179231305 chr5:179231022-179231032
8	NR2F2	chr5:179230877-179231324	K562	blood:	n/a	n/a
9	POLR2A	chr5:179229487-179231518	GM12878	blood:	n/a	n/a
10	POLR2A	chr5:179230529-179231504	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr5:179230661-179231271	U87	brain:	n/a	n/a
12	POLR2A	chr5:179224667-179233676	HL-60	blood:	n/a	n/a
13	POLR2A	chr5:179230590-179233696	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr5:179230263-179231585	GM12878	blood:	n/a	n/a
15	RUNX3	chr5:179230923-179231312	GM12878	blood:	n/a	chr5:179231130-179231145
16	POLR2A	chr5:179230976-179231284	HCT-116	colon:	n/a	n/a
17	POLR2A	chr5:179230770-179234550	Hela-S3	cervix:	n/a	n/a
18	MXI1	chr5:179230515-179231399	IMR90	lung:	n/a	n/a
19	RUNX3	chr5:179230963-179231313	GM12878	blood:	n/a	chr5:179231130-179231145
20	POLR2A	chr5:179230587-179231821	K562	blood:	n/a	n/a
21	POLR2A	chr5:179229886-179231742	HL-60	blood:	n/a	n/a
22	POLR2A	chr5:179231152-179231263	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr5:179230915-179231376	ProgFib	skin:	n/a	n/a
24	POLR2A	chr5:179230716-179231337	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr5:179230312-179231393	Hela-S3	cervix:	n/a	n/a
26	ELF1	chr5:179231175-179231822	GM12878	blood:	n/a	n/a
27	POLR2A	chr5:179230615-179231365	HepG2	liver:	n/a	n/a
28	POLR2A	chr5:179228473-179231388	HepG2	liver:	n/a	n/a
29	POLR2A	chr5:179228779-179234761	K562	blood:	n/a	n/a
30	BHLHE40	chr5:179231154-179231372	K562	blood:	n/a	n/a
31	POLR2A	chr5:179230730-179231952	MCF10A-Er-Src	breast:	n/a	n/a
32	MAX	chr5:179230988-179231258	K562	blood:	n/a	chr5:179231022-179231032
33	POLR2A	chr5:179229521-179234618	MCF-7	breast:	n/a	n/a
34	POLR2A	chr5:179230582-179232017	K562	blood:	n/a	n/a
35	POLR2A	chr5:179230889-179231259	U87	brain:	n/a	n/a
36	RCOR1	chr5:179230963-179231273	K562	blood:	n/a	n/a
37	MAX	chr5:179230641-179231360	K562	blood:	n/a	chr5:179231289-179231305 chr5:179231022-179231032
38	POLR2A	chr5:179230782-179231678	HepG2	liver:	n/a	n/a
39	ZMIZ1	chr5:179231156-179231338	K562	blood:	n/a	n/a
40	POLR2A	chr5:179231005-179231335	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr5:179224688-179234670	K562	blood:	n/a	n/a
42	HEY1	chr5:179230758-179231329	K562	blood:	n/a	n/a
43	POLR2A	chr5:179231030-179231289	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:179158622..179161306-chr5:179229255..179232070,3	MCF-7	breast:
2	chr5:179229039..179235504-chr5:179284286..179287391,9	MCF-7	breast:
3	chr5:179231022..179234564-chr5:179332456..179334964,4	MCF-7	breast:
4	chr5:179227831..179231343-chr5:179333679..179336075,3	MCF-7	breast:
5	chr5:179048743..179051829-chr5:179229515..179233744,4	MCF-7	breast:
6	chr5:179159678..179161359-chr5:179228559..179231556,2	MCF-7	breast:
7	chr5:179189775..179190581-chr5:179231187..179232028,2	K562	blood:
8	chr5:179049028..179050758-chr5:179230503..179232044,2	K562	blood:
9	chr5:179194648..179196545-chr5:179230223..179233407,4	K562	blood:

No data

Variant related genes	Relation type
MGAT4B	TF binding region
SQSTM1	TF binding region
ENSG00000245317	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000161010	Chromatin interaction
ENSG00000197226	Chromatin interaction
ENSG00000169045	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1019443	0.91[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10516146	0.81[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs11744662	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs12374446	0.81[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs12522926	0.81[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13182141	0.86[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.92[YRI][hapmap]
rs34646062	0.80[LWK][hapmap];1.00[YRI][hapmap]
rs3797774	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs6601073	0.81[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs7736300	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv883275	chr5:179193598-179267783	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
7	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
8	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
9	nsv823361	chr5:179213324-179251243	Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
10	nsv600660	chr5:179214251-179231248	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
11	nsv883278	chr5:179214818-179238794	Active TSS Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
12	nsv883279	chr5:179214818-179248774	Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
13	nsv870188	chr5:179218824-179235424	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
14	nsv600662	chr5:179220010-179231248	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
15	nsv883280	chr5:179220010-179238794	Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
16	nsv883281	chr5:179220010-179250500	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
17	nsv883282	chr5:179220638-179231248	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
18	nsv883283	chr5:179220638-179231681	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
19	nsv883284	chr5:179220638-179246415	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	158 gene(s)	inside rSNPs	diseases
20	nsv600665	chr5:179221789-179231248	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
21	nsv600666	chr5:179221789-179231681	Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
22	nsv883285	chr5:179223023-179238794	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	153 gene(s)	inside rSNPs	diseases
23	nsv600668	chr5:179227865-179242581	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12652934	BTNL3	cis	parietal	SCAN
rs12652934	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL
rs12652934	TBC1D9B,LOC153811	cis	brain	BrainEAC
rs12652934	CANX	cis	cerebellum	SCAN
rs12652934	CANX	cis	parietal	SCAN
rs12652934	C5orf45	cis	cerebellum	SCAN
rs12652934	MAPK9	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179223800-179231600	Weak transcription	Fetal Kidney	kidney
2	chr5:179223800-179231600	Weak transcription	Psoas Muscle	Psoas
3	chr5:179224000-179232200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr5:179226200-179232200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:179226800-179233200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:179227200-179231800	Weak transcription	Brain Substantia Nigra	brain
7	chr5:179227600-179232000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr5:179227800-179232000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:179227800-179232200	Enhancers	Fetal Heart	heart
10	chr5:179228000-179232400	Weak transcription	Aorta	Aorta
11	chr5:179228400-179232400	Genic enhancers	Placenta	Placenta
12	chr5:179228600-179231400	Weak transcription	Fetal Brain Female	brain
13	chr5:179228600-179232200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:179228800-179231400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:179228800-179231400	Enhancers	Right Ventricle	heart
16	chr5:179228800-179231600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr5:179228800-179231600	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr5:179228800-179231600	Genic enhancers	Fetal Intestine Small	intestine
19	chr5:179228800-179231800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr5:179228800-179231800	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr5:179228800-179232000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:179228800-179232000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr5:179228800-179232000	Enhancers	Brain Hippocampus Middle	brain
24	chr5:179228800-179232000	Genic enhancers	Fetal Stomach	stomach
25	chr5:179228800-179232200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr5:179228800-179232200	Genic enhancers	Fetal Muscle Trunk	muscle
27	chr5:179228800-179232400	Enhancers	Primary B cells from peripheral blood	blood
28	chr5:179228800-179232400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr5:179228800-179232400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:179228800-179232400	Enhancers	Fetal Thymus	thymus
31	chr5:179229000-179231400	Enhancers	Stomach Mucosa	stomach
32	chr5:179229000-179231600	Genic enhancers	NHLF	lung
33	chr5:179229000-179231800	Enhancers	Colon Smooth Muscle	Colon
34	chr5:179229000-179232000	Enhancers	Pancreas	Pancrea
35	chr5:179229200-179231800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:179229200-179231800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr5:179229200-179231800	Enhancers	HMEC	breast
38	chr5:179229200-179232000	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr5:179229400-179232200	Enhancers	Left Ventricle	heart
40	chr5:179229400-179232400	Enhancers	Primary B cells from cord blood	blood
41	chr5:179229600-179231800	Enhancers	Fetal Intestine Large	intestine
42	chr5:179229600-179232000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr5:179229600-179232000	Enhancers	NH-A	brain
44	chr5:179229600-179232200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:179229800-179231600	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr5:179229800-179231800	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr5:179229800-179231800	Enhancers	NHEK	skin
48	chr5:179230000-179231800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr5:179230000-179231800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr5:179230000-179231800	Enhancers	Osteobl	bone

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