Variant report

Variant	rs4666436
Chromosome Location	chr2:20795945-20795946
allele	C/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	EP300	chr2:20795646-20795967	HepG2	liver:	n/a	n/a
2	NFYA	chr2:20795726-20795974	Hela-S3	cervix:	n/a	n/a
3	RCOR1	chr2:20794926-20796101	GM12878	blood:	n/a	n/a
4	POU2F2	chr2:20795167-20795952	GM12878	blood:	n/a	chr2:20795447-20795469 chr2:20795454-20795464 chr2:20795454-20795464 chr2:20795453-20795465 chr2:20795455-20795462 chr2:20795451-20795466 chr2:20795451-20795465 chr2:20795454-20795463
5	CUX1	chr2:20795282-20796038	GM12878	blood:	n/a	n/a
6	MAFK	chr2:20795591-20796042	HepG2	liver:	n/a	n/a
7	MEF2C	chr2:20795096-20795960	GM12878	blood:	n/a	chr2:20795435-20795443
8	POLR2A	chr2:20795645-20796014	K562	blood:	n/a	n/a
9	POLR2A	chr2:20795002-20796171	GM12891	blood:	n/a	n/a
10	YY1	chr2:20795141-20795977	GM12878	blood:	n/a	chr2:20795382-20795404
11	CTCF	chr2:20795860-20796010	HCPEpiC	choroid plexus:	n/a	n/a
12	BCL11A	chr2:20795157-20796071	GM12878	blood:	n/a	n/a
13	MAX	chr2:20795325-20795957	K562	blood:	n/a	chr2:20795679-20795688
14	POLR2A	chr2:20795052-20795989	GM12891	blood:	n/a	n/a
15	SP1	chr2:20795158-20796053	GM12878	blood:	n/a	chr2:20795176-20795190
16	RAD21	chr2:20795460-20795977	IMR90	lung:	n/a	chr2:20795539-20795551 chr2:20795516-20795535
17	RELA	chr2:20794814-20796033	GM10847	blood:	n/a	n/a
18	CTCF	chr2:20795940-20796090	HBMEC	blood vessel:	n/a	n/a
19	BCLAF1	chr2:20795035-20796067	GM12878	blood:	n/a	n/a
20	CBX3	chr2:20795041-20796175	K562	blood:	n/a	n/a
21	BATF	chr2:20795557-20796007	GM12878	blood:	n/a	chr2:20795865-20795875
22	FOS	chr2:20795717-20796030	MCF10A-Er-Src	breast:	n/a	chr2:20795868-20795876
23	PML	chr2:20794992-20796252	GM12878	blood:	n/a	n/a
24	MYBL2	chr2:20795354-20797572	HepG2	liver:	n/a	n/a
25	MAFF	chr2:20795737-20795950	K562	blood:	n/a	n/a
26	MAFK	chr2:20795399-20796016	IMR90	lung:	n/a	n/a
27	MAFK	chr2:20795714-20795970	HepG2	liver:	n/a	n/a
28	ZBTB7A	chr2:20795835-20796014	K562	blood:	n/a	n/a
29	RELA	chr2:20795043-20796237	GM19099	blood:	n/a	n/a
30	ZNF384	chr2:20795880-20796049	K562	blood:	n/a	n/a
31	FOS	chr2:20795640-20796064	HUVEC	blood vessel:	n/a	chr2:20795868-20795876
32	TAF1	chr2:20795706-20796072	K562	blood:	n/a	n/a
33	MXI1	chr2:20795121-20796144	GM12878	blood:	n/a	n/a
34	NFIC	chr2:20795087-20796145	GM12878	blood:	n/a	n/a
35	POU2F2	chr2:20795054-20796102	GM12878	blood:	n/a	chr2:20795447-20795469 chr2:20795454-20795464 chr2:20795454-20795464 chr2:20795453-20795465 chr2:20795455-20795462 chr2:20795451-20795466 chr2:20795451-20795465 chr2:20795454-20795463
36	POLR2A	chr2:20795025-20796124	GM12878	blood:	n/a	n/a
37	ZNF143	chr2:20795071-20796419	GM12878	blood:	n/a	chr2:20795525-20795543
38	POLR2A	chr2:20795052-20796005	GM12892	blood:	n/a	n/a
39	NR2F2	chr2:20795020-20796228	K562	blood:	n/a	chr2:20795628-20795643
40	FOS	chr2:20795675-20795976	MCF10A-Er-Src	breast:	n/a	chr2:20795868-20795876
41	IRF4	chr2:20795065-20796082	GM12878	blood:	n/a	n/a
42	TBP	chr2:20795135-20796073	GM12878	blood:	n/a	n/a
43	MAX	chr2:20795108-20796060	K562	blood:	n/a	chr2:20795679-20795688
44	CTCF	chr2:20795880-20796030	GM12873	blood:	n/a	n/a
45	STAT5A	chr2:20794804-20796454	GM12878	blood:	n/a	chr2:20795134-20795142 chr2:20795900-20795912 chr2:20795532-20795544
46	RELA	chr2:20795106-20796552	GM18505	blood:	n/a	n/a
47	EBF1	chr2:20794957-20796053	GM12878	blood:	n/a	chr2:20795594-20795605 chr2:20795237-20795247
48	PAX5	chr2:20795085-20795985	GM12878	blood:	n/a	chr2:20795677-20795695
49	RUNX3	chr2:20794905-20796091	GM12878	blood:	n/a	n/a
50	TCF7L2	chr2:20795312-20795950	HCT-116	colon:	n/a	chr2:20795731-20795740 chr2:20795733-20795740

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:20795912-20795962	GM19239	blood:	n/a
2	chr2:20795912-20795962	MCF-7	breast:	n/a
3	chr2:20795912-20795962	PANC-1	pancreas:	n/a
4	chr2:20795912-20795962	AG09309	skin:	n/a
5	chr2:20795912-20795962	GM12892	blood:	n/a
6	chr2:20795912-20795962	SAEC	small airway:	n/a
7	chr2:20795912-20795962	SK-N-SH	brain:	n/a
8	chr2:20795912-20795962	AG10803	skin:	n/a
9	chr2:20795912-20795962	ProgFib	skin:	n/a
10	chr2:20795912-20795962	ovcar-3	ovarian:	n/a
11	chr2:20795912-20795962	Hela-S3	cervix:	n/a
12	chr2:20795912-20795962	RPTEC	kidney:	n/a
13	chr2:20795912-20795962	HMEC	breast:	n/a
14	chr2:20795912-20795962	HNPCEpiC	eye:	n/a
15	chr2:20795912-20795962	HCM	heart:	n/a
16	chr2:20795912-20795962	HRCEpiC	kidney:	n/a
17	chr2:20795912-20795962	LNCaP	prostate:	n/a
18	chr2:20795912-20795962	HRPEpiC	eye:	n/a
19	chr2:20795912-20795962	HCF	heart:	n/a
20	chr2:20795912-20795962	GM12891	blood:	n/a
21	chr2:20795912-20795962	T-47D	breast:	n/a
22	chr2:20795912-20795962	AG04450	lung:	fetal
23	chr2:20795912-20795962	ECC-1	luminal epithelium:	n/a
24	chr2:20795912-20795962	Hepatocyte	liver:	n/a
25	chr2:20795912-20795962	GM12878	blood:	n/a
26	chr2:20795912-20795962	NH-A	brain:	n/a
27	chr2:20795912-20795962	HEK293	kidney:	embryo
28	chr2:20795912-20795962	AG09319	gingival:	n/a
29	chr2:20795912-20795962	HUVEC	blood vessel:	n/a
30	chr2:20795912-20795962	NHBE	bronchial:	n/a
31	chr2:20795912-20795962	A549	lung:	n/a
32	chr2:20795912-20795962	PrEC	prostate:	n/a
33	chr2:20795912-20795962	AoSMC	blood vessel:	n/a
34	chr2:20795912-20795962	NHDF-neo	bronchial:	n/a
35	chr2:20795912-20795962	PFSK-1	brain:	n/a
36	chr2:20795912-20795962	Caco-2	colon:	n/a
37	chr2:20795912-20795962	IMR90	lung:	fetal
38	chr2:20795912-20795962	HAEpiC	amniotic membrane:	n/a
39	chr2:20795912-20795962	CMK	blood:	n/a
40	chr2:20795912-20795962	NT2-D1	testis:	n/a
41	chr2:20795912-20795962	HCPEpiC	choroid plexus:	n/a
42	chr2:20795912-20795962	SK-N-MC	brain:	n/a
43	chr2:20795912-20795962	NB4	blood:	n/a
44	chr2:20795912-20795962	HRE	kidney:	n/a
45	chr2:20795912-20795962	HEEpiC	esophagus:	n/a
46	chr2:20795912-20795962	HepG2	liver:	n/a
47	chr2:20795912-20795962	HL-60	blood:	n/a
48	chr2:20795912-20795962	MCF10A-Er-Src	breast:	n/a
49	chr2:20795912-20795962	BE2_C	brain:	n/a
50	chr2:20795912-20795962	Jurkat	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20666213..20668504-chr2:20794709..20797277,2	MCF-7	breast:
2	chr2:20644797..20655251-chr2:20787626..20802274,53	MCF-7	breast:
3	chr2:20790810..20793188-chr2:20795452..20798408,2	MCF-7	breast:
4	chr2:20793781..20795387-chr2:20795652..20798532,2	K562	blood:
5	chr2:20767266..20769028-chr2:20793726..20796533,2	K562	blood:
6	chr2:20794523..20801165-chr2:20801395..20807064,11	K562	blood:
7	chr2:20795835..20797595-chr2:20834654..20837275,2	K562	blood:
8	chr2:20790147..20792298-chr2:20794346..20796797,2	K562	blood:
9	chr2:20767266..20769707-chr2:20793726..20796533,3	K562	blood:
10	chr2:20644186..20651576-chr2:20790196..20799394,18	MCF-7	breast:

Variant related genes	Relation type
HS1BP3-IT1	TF binding region
HS1BP3-IT1	CpG island
ENSG00000233416	Chromatin interaction
ENSG00000231948	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000143878	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10153843	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10166792	0.80[JPT][hapmap]
rs10177834	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10195722	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs11096679	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11885969	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472478	0.85[CHB][hapmap]
rs12621527	0.86[CHB][hapmap]
rs13013281	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13031724	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032956	0.94[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1466200	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16987880	0.81[JPT][hapmap]
rs16987884	0.81[JPT][hapmap]
rs4666430	0.86[CHB][hapmap]
rs4666431	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs57734601	0.83[ASN][1000 genomes]
rs6712435	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6715159	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6722960	0.88[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs921599	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv581167	chr2:20791125-20827846	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4666436	C2orf43	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20785000-20796000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:20785800-20796000	Weak transcription	Aorta	Aorta
3	chr2:20786200-20797600	Weak transcription	Psoas Muscle	Psoas
4	chr2:20787200-20800200	Enhancers	Right Ventricle	heart
5	chr2:20789000-20798200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:20789200-20797000	Enhancers	Spleen	Spleen
7	chr2:20789200-20800400	Enhancers	Placenta	Placenta
8	chr2:20790200-20797800	Enhancers	Fetal Intestine Large	intestine
9	chr2:20790800-20801200	Enhancers	Adipose Nuclei	Adipose
10	chr2:20791200-20796600	Weak transcription	Fetal Heart	heart
11	chr2:20791400-20796600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:20791800-20796400	Weak transcription	Pancreas	Pancrea
13	chr2:20791800-20797200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr2:20791800-20800400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr2:20792000-20797800	Enhancers	HSMM	muscle
16	chr2:20792000-20798200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr2:20792200-20797800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:20792200-20797800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:20792200-20797800	Enhancers	NH-A	brain
20	chr2:20792200-20798200	Enhancers	Ovary	ovary
21	chr2:20792400-20797600	Enhancers	A549	lung
22	chr2:20792400-20797800	Enhancers	Lung	lung
23	chr2:20792400-20797800	Enhancers	NHLF	lung
24	chr2:20792400-20798400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr2:20792400-20800200	Enhancers	Right Atrium	heart
26	chr2:20792600-20797200	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr2:20792600-20797800	Enhancers	NHDF-Ad	bronchial
28	chr2:20792800-20797200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:20792800-20798200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:20792800-20801800	Enhancers	HUVEC	blood vessel
31	chr2:20793000-20797800	Enhancers	Brain Hippocampus Middle	brain
32	chr2:20793000-20799000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr2:20793000-20800400	Enhancers	Left Ventricle	heart
34	chr2:20793000-20801200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:20793200-20796200	Enhancers	Liver	Liver
36	chr2:20793400-20796200	Weak transcription	Fetal Lung	lung
37	chr2:20793400-20797600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:20793600-20797400	Enhancers	Primary B cells from peripheral blood	blood
39	chr2:20793600-20797600	Enhancers	K562	blood
40	chr2:20793800-20801400	Enhancers	Brain Angular Gyrus	brain
41	chr2:20794000-20796000	Weak transcription	Stomach Mucosa	stomach
42	chr2:20794000-20797200	Enhancers	Osteobl	bone
43	chr2:20794200-20798000	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr2:20794200-20800000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:20794400-20796400	Weak transcription	Gastric	stomach
46	chr2:20794600-20796200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:20794600-20796200	Flanking Active TSS	GM12878-XiMat	blood
48	chr2:20794600-20796200	Enhancers	HSMMtube	muscle
49	chr2:20794600-20797400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:20794600-20798200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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