Variant report

Variant	rs1165679
Chromosome Location	chr12:104323238-104323239
allele	A/C
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	GABPA	chr12:104322837-104324464	SK-N-SH	brain:	n/a	chr12:104323616-104323625 chr12:104324137-104324146
2	ZNF143	chr12:104322493-104324458	GM12878	blood:	n/a	chr12:104324141-104324159 chr12:104323579-104323597 chr12:104323586-104323595 chr12:104323536-104323554 chr12:104324136-104324146 chr12:104323540-104323559 chr12:104324429-104324447
3	ELF1	chr12:104323019-104323373	K562	blood:	n/a	chr12:104323287-104323296
4	EBF1	chr12:104322093-104325000	GM12878	blood:	n/a	n/a
5	IRF1	chr12:104323129-104324338	K562	blood:	n/a	chr12:104324147-104324156 chr12:104323289-104323303
6	RUNX3	chr12:104321971-104325533	GM12878	blood:	n/a	n/a
7	BCL3	chr12:104322865-104324368	A549	lung:	n/a	chr12:104323616-104323629 chr12:104323586-104323594 chr12:104323615-104323624 chr12:104323613-104323626
8	CHD2	chr12:104323166-104325167	Hela-S3	cervix:	n/a	chr12:104324650-104324660
9	MTA3	chr12:104322308-104323916	GM12878	blood:	n/a	n/a
10	MEF2A	chr12:104322248-104323544	GM12878	blood:	n/a	n/a
11	BCLAF1	chr12:104322139-104323932	GM12878	blood:	n/a	chr12:104323616-104323629 chr12:104323586-104323594 chr12:104323615-104323624 chr12:104323613-104323626
12	POLR2A	chr12:104322428-104325591	SK-N-MC	brain:	n/a	n/a
13	WRNIP1	chr12:104322092-104325599	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:104322636-104323705	GM12878	blood:	n/a	n/a
15	NFIC	chr12:104322006-104324995	GM12878	blood:	n/a	n/a
16	YY1	chr12:104322704-104323310	GM12878	blood:	n/a	chr12:104323287-104323301
17	JUND	chr12:104322907-104324569	A549	lung:	n/a	chr12:104324044-104324053 chr12:104323621-104323630 chr12:104323993-104324002 chr12:104323613-104323622 chr12:104324060-104324069 chr12:104323617-104323626 chr12:104323618-104323627
18	YY1	chr12:104322867-104324436	GM12892	blood:	n/a	chr12:104323616-104323625 chr12:104323613-104323622 chr12:104323287-104323301 chr12:104323621-104323630 chr12:104323613-104323624 chr12:104323626-104323634
19	TAF1	chr12:104322935-104323533	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:104322498-104325320	GM12878	blood:	n/a	n/a
21	FOXM1	chr12:104322048-104323502	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:104323070-104323641	HCT-116	colon:	n/a	n/a
23	ZBTB7A	chr12:104323102-104323385	HepG2	liver:	n/a	n/a
24	MYC	chr12:104322591-104324497	K562	blood:	n/a	chr12:104324136-104324146 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104324369-104324379
25	MAX	chr12:104322072-104325169	GM12878	blood:	n/a	chr12:104324136-104324146 chr12:104322562-104322569 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104322561-104322572 chr12:104324369-104324379
26	GABPA	chr12:104323118-104323377	HepG2	liver:	n/a	n/a
27	TAF1	chr12:104322790-104323593	GM12891	blood:	n/a	n/a
28	ELF1	chr12:104323053-104324268	A549	lung:	n/a	chr12:104323827-104323838 chr12:104323825-104323838 chr12:104323287-104323296
29	MXI1	chr12:104323090-104325397	Hela-S3	cervix:	n/a	chr12:104323780-104323795 chr12:104323778-104323793
30	MYC	chr12:104323016-104325167	K562	blood:	n/a	chr12:104324136-104324146 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104324369-104324379
31	ETS1	chr12:104323211-104324491	K562	blood:	n/a	chr12:104323829-104323846 chr12:104324054-104324067 chr12:104323829-104323838 chr12:104323829-104323838 chr12:104324145-104324156 chr12:104323616-104323627 chr12:104323830-104323840 chr12:104324052-104324067 chr12:104323829-104323846 chr12:104323585-104323598 chr12:104324137-104324148 chr12:104323586-104323599 chr12:104323829-104323838
32	GABPA	chr12:104323008-104324431	SK-N-SH	brain:	n/a	chr12:104323616-104323625 chr12:104324137-104324146
33	TAF1	chr12:104323059-104323337	HepG2	liver:	n/a	n/a
34	RELA	chr12:104321990-104325291	GM19193	blood:	n/a	n/a
35	SIX5	chr12:104322968-104324401	A549	lung:	n/a	chr12:104323586-104323595 chr12:104323588-104323597 chr12:104323585-104323599
36	POU2F2	chr12:104322391-104323600	GM12878	blood:	n/a	n/a
37	UBTF	chr12:104323087-104323487	K562	blood:	n/a	n/a
38	POLR2A	chr12:104323105-104323590	ProgFib	skin:	n/a	n/a
39	CREB1	chr12:104322959-104324558	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr12:104322422-104323610	GM12892	blood:	n/a	n/a
41	ZNF143	chr12:104323002-104324370	K562	blood:	n/a	chr12:104324141-104324159 chr12:104323579-104323597 chr12:104323586-104323595 chr12:104323536-104323554 chr12:104324136-104324146 chr12:104323540-104323559
42	ZBTB33	chr12:104323232-104324203	A549	lung:	n/a	n/a
43	SIN3AK20	chr12:104323076-104323614	HepG2	liver:	n/a	n/a
44	MAX	chr12:104322913-104325128	Hela-S3	cervix:	n/a	chr12:104324136-104324146 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104324369-104324379
45	NFIC	chr12:104322910-104323604	HepG2	liver:	n/a	n/a
46	MAX	chr12:104322651-104325593	A549	lung:	n/a	chr12:104324136-104324146 chr12:104324993-104325000 chr12:104324419-104324429 chr12:104323780-104323789 chr12:104324642-104324652 chr12:104323784-104323793 chr12:104323936-104323951 chr12:104324369-104324379
47	GTF2F1	chr12:104322937-104324405	Hela-S3	cervix:	n/a	n/a
48	CREB1	chr12:104322814-104325148	HepG2	liver:	n/a	n/a
49	E2F6	chr12:104322797-104325182	K562	blood:	n/a	chr12:104324137-104324146 chr12:104324434-104324444 chr12:104323616-104323625 chr12:104323708-104323719
50	MYC	chr12:104322649-104323503	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:109642498..109643231-chr12:104323072..104323792,2	Hela-S3	cervix:
2	chr11:62608620..62609147-chr12:104322726..104323477,2	NB4	blood:
3	chr12:104298858..104303101-chr12:104321689..104325332,4	K562	blood:
4	chr12:104320418..104331406-chr12:104346801..104355501,25	MCF-7	breast:
5	chr12:104233909..104239694-chr12:104322835..104327398,8	K562	blood:
6	chr12:104323141..104323941-chr5:162886624..162887510,2	Hela-S3	cervix:
7	chr12:104314809..104316668-chr12:104321304..104323532,2	MCF-7	breast:
8	chr12:104233715..104236918-chr12:104321893..104325386,6	K562	blood:
9	chr12:104319225..104328292-chr12:104356282..104362179,14	K562	blood:
10	chr12:104322684..104325586-chr12:104530441..104532019,2	K562	blood:
11	chr12:104276117..104279238-chr12:104322705..104326968,4	K562	blood:
12	chr12:104322943..104325215-chr12:104358408..104360868,4	MCF-7	breast:
13	chr12:104309007..104311155-chr12:104321580..104324192,3	K562	blood:
14	chr12:104313655..104316610-chr12:104321073..104323844,5	MCF-7	breast:
15	chr12:104317968..104319875-chr12:104322035..104323737,2	MCF-7	breast:
16	chr12:104300678..104303599-chr12:104319392..104323559,4	K562	blood:
17	chr12:104294934..104297771-chr12:104321554..104323667,2	MCF-7	breast:

Variant related genes	Relation type
MIR3652	TF binding region
HSP90B1	TF binding region
ENSG00000270066	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000139372	Chromatin interaction
ENSG00000170584	Chromatin interaction
ENSG00000072571	Chromatin interaction
ENSG00000204954	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1007652	0.88[AMR][1000 genomes]
rs10745985	1.00[ASW][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861111	1.00[ASN][1000 genomes]
rs11612613	1.00[LWK][hapmap];0.91[MKK][hapmap]
rs1165595	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165667	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165671	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165683	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809773	1.00[ASN][1000 genomes]
rs12813601	1.00[ASN][1000 genomes]
rs12819539	1.00[ASN][1000 genomes]
rs12823195	1.00[ASN][1000 genomes]
rs17034955	1.00[ASN][1000 genomes]
rs1866075	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992208	0.83[TSI][hapmap]
rs2255584	0.83[TSI][hapmap]
rs2255791	0.83[TSI][hapmap]
rs2255794	0.83[TSI][hapmap]
rs2255795	0.83[TSI][hapmap]
rs2255797	0.83[TSI][hapmap]
rs2438111	0.83[TSI][hapmap]
rs2576953	1.00[ASN][1000 genomes]
rs2576956	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576959	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576968	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2576976	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583238	1.00[CEU][hapmap]
rs2722172	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2919806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34309392	1.00[ASN][1000 genomes]
rs34811234	1.00[ASN][1000 genomes]
rs34863477	1.00[ASN][1000 genomes]
rs35392305	1.00[ASN][1000 genomes]
rs35642814	1.00[ASN][1000 genomes]
rs35822062	1.00[ASN][1000 genomes]
rs35844634	1.00[ASN][1000 genomes]
rs4964197	1.00[ASN][1000 genomes]
rs61939568	1.00[ASN][1000 genomes]
rs71466284	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71466286	1.00[ASN][1000 genomes]
rs71466293	1.00[ASN][1000 genomes]
rs73175816	1.00[ASN][1000 genomes]
rs9669259	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9669708	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1165679	MIR3652	cis	Artery Tibial	GTEx
rs1165679	MIR3652	cis	Esophagus Muscularis	GTEx
rs1165679	MIR3652	cis	Nerve Tibial	GTEx
rs1165679	MIR3652	cis	Whole Blood	GTEx
rs1165679	MIR3652	cis	Adipose Subcutaneous	GTEx
rs1165679	MIR3652	cis	Thyroid	GTEx
rs1165679	MIR3652	cis	Muscle Skeletal	GTEx
rs1165679	NT5DC3	cis	parietal	SCAN
rs1165679	MIR3652	cis	Esophagus Mucosa	GTEx
rs1165679	SLC41A2	cis	parietal	SCAN
rs1165679	GLT8D2	cis	parietal	SCAN
rs1165679	MIR3652	cis	Stomach	GTEx
rs1165679	MIR3652	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104322000-104323400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr12:104322000-104323600	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr12:104322000-104323600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:104322000-104323600	Flanking Active TSS	Fetal Thymus	thymus
5	chr12:104322000-104325000	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr12:104322000-104325200	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr12:104322000-104325200	Active TSS	Rectal Smooth Muscle	rectum
8	chr12:104322200-104323400	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr12:104322200-104323400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr12:104322200-104323400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:104322200-104323400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr12:104322200-104324800	Active TSS	Thymus	Thymus
13	chr12:104322200-104325200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr12:104322200-104325200	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr12:104322200-104326200	Active TSS	H1 Cell Line	embryonic stem cell
16	chr12:104322200-104326200	Active TSS	GM12878-XiMat	blood
17	chr12:104322400-104323400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr12:104322400-104323400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:104322400-104323600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr12:104322400-104325200	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr12:104322400-104325200	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr12:104322400-104325200	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr12:104322400-104325400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:104322400-104325600	Active TSS	H9 Cell Line	embryonic stem cell
25	chr12:104322400-104325800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr12:104322400-104326000	Active TSS	Colonic Mucosa	Colon
27	chr12:104322400-104326000	Active TSS	Fetal Intestine Small	intestine
28	chr12:104322400-104327000	Active TSS	Right Atrium	heart
29	chr12:104322600-104323400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
30	chr12:104322600-104323400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr12:104322600-104323400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr12:104322600-104323400	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr12:104322600-104323400	Flanking Active TSS	HMEC	breast
34	chr12:104322600-104323400	Flanking Active TSS	NHEK	skin
35	chr12:104322600-104323600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:104322600-104324800	Active TSS	Primary B cells from peripheral blood	blood
37	chr12:104322600-104325000	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr12:104322600-104325200	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr12:104322600-104325200	Active TSS	Brain Substantia Nigra	brain
40	chr12:104322600-104325400	Active TSS	Brain Hippocampus Middle	brain
41	chr12:104322600-104325400	Active TSS	Gastric	stomach
42	chr12:104322600-104325400	Active TSS	Placenta Amnion	Placenta Amnion
43	chr12:104322600-104325600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:104322600-104325600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr12:104322600-104325600	Active TSS	Esophagus	oesophagus
46	chr12:104322600-104325600	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr12:104322600-104325800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:104322600-104325800	Active TSS	Fetal Muscle Trunk	muscle
49	chr12:104322600-104326400	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr12:104322600-104327000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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